--- /dev/null
+30.09.03: fixed bugs in pipeline (truncated long sequences by 20 bytes)!
--- /dev/null
+#!/usr/bin/python
+# Copyright (C) 2004 Rune Linding & Lars Juhl Jensen - EMBL
+# The DisEMBL is licensed under the GPL license
+# (http://www.opensource.org/licenses/gpl-license.php)
+# DisEMBL pipeline
+
+
+from string import *
+import sys,re
+from sys import argv
+import os
+from os import system,popen3
+
+relpath = re.sub("/DisEMBL.py$","",argv[0])
+cwd = re.sub("/$","", os.getcwd())
+newpath =cwd+"/"+relpath+"/biopython-1.50"
+sys.path.append(newpath)
+
+from Bio import File
+from Bio import Fasta
+
+
+import fpformat
+import tempfile
+
+
+# change these to the correct paths
+NN_bin = relpath + "/" + 'disembl'
+SG_bin = relpath + "/" + 'sav_gol'
+
+def JensenNet(sequence):
+ outFile = tempfile.mktemp()
+ inFile= tempfile.mktemp()
+ open(inFile,'w').write(sequence+'\n')
+ system(NN_bin + '< ' + inFile +' > ' + outFile)
+ REM465 = []
+ COILS = []
+ HOTLOOPS = []
+ resultsFile = open(outFile,'r')
+ results = resultsFile.readlines()
+ resultsFile.close()
+ for result in results:
+ coil = float(fpformat.fix(split(result)[0],6))
+ COILS.append(coil)
+ hotloop = float(fpformat.fix(split(result)[1],6))
+ HOTLOOPS.append(hotloop)
+ rem465 = float(fpformat.fix(split(result)[2],6))
+ REM465.append(rem465)
+ os.remove(inFile)
+ os.remove(outFile)
+ return COILS, HOTLOOPS, REM465
+
+
+def SavitzkyGolay(window,derivative,datalist):
+ if len(datalist) < 2*window:
+ window = len(datalist)/2
+ elif window == 0:
+ window = 1
+ stdin, stdout, stderr = popen3(SG_bin + ' -V0 -D' + str(derivative) + ' -n' + str(window)+','+str(window))
+ for data in datalist:
+ stdin.write(`data`+'\n')
+ try:
+ stdin.close()
+ except:
+ print stderr.readlines()
+ results = stdout.readlines()
+ stdout.close()
+ SG_results = []
+ for result in results:
+ f = float(fpformat.fix(result,6))
+ if f < 0:
+ SG_results.append(0)
+ else:
+ SG_results.append(f)
+ return SG_results
+
+def getSlices(NNdata, fold, join_frame, peak_frame, expect_val):
+ slices = []
+ inSlice = 0
+ for i in range(len(NNdata)):
+ if inSlice:
+ if NNdata[i] < expect_val:
+ if maxSlice >= fold*expect_val:
+ slices.append([beginSlice, endSlice])
+ inSlice = 0
+ else:
+ endSlice += 1
+ if NNdata[i] > maxSlice:
+ maxSlice = NNdata[i]
+ elif NNdata[i] >= expect_val:
+ beginSlice = i
+ endSlice = i
+ inSlice = 1
+ maxSlice = NNdata[i]
+ if inSlice and maxSlice >= fold*expect_val:
+ slices.append([beginSlice, endSlice])
+
+ i = 0
+ while i < len(slices):
+ if i+1 < len(slices) and slices[i+1][0]-slices[i][1] <= join_frame:
+ slices[i] = [ slices[i][0], slices[i+1][1] ]
+ del slices[i+1]
+ elif slices[i][1]-slices[i][0]+1 < peak_frame:
+ del slices[i]
+ else:
+ i += 1
+ return slices
+
+
+def reportSlicesTXT(slices, sequence):
+ if slices == []:
+ s = lower(sequence)
+ else:
+ if slices[0][0] > 0:
+ s = lower(sequence[0:slices[0][0]])
+ else:
+ s = ''
+ for i in range(len(slices)):
+ if i > 0:
+ sys.stdout.write(', ')
+ sys.stdout.write( str(slices[i][0]+1) + '-' + str(slices[i][1]+1) )
+ s = s + upper(sequence[slices[i][0]:(slices[i][1]+1)])
+ if i < len(slices)-1:
+ s = s + lower(sequence[(slices[i][1]+1):(slices[i+1][0])])
+ elif slices[i][1] < len(sequence)-1:
+ s = s + lower(sequence[(slices[i][1]+1):(len(sequence))])
+ print ''
+ print s
+
+
+
+def runDisEMBLpipeline():
+ try:
+ smooth_frame = int(sys.argv[1])
+ peak_frame = int(sys.argv[2])
+ join_frame = int(sys.argv[3])
+ fold_coils = float(sys.argv[4])
+ fold_hotloops = float(sys.argv[5])
+ fold_rem465 = float(sys.argv[6])
+ #file = str(sys.argv[7])
+ try:
+ mode = sys.argv[7]
+ except:
+ mode = 'default'
+ except:
+ print '\nDisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file [mode]\n'
+ print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file'
+ print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB seperated format'
+ raise SystemExit
+ db = sys.stdin
+ parser = Fasta.RecordParser()
+ iterator = Fasta.Iterator(db,parser)
+ while 1:
+ try:
+ cur_record = iterator.next()
+ sequence = upper(cur_record.sequence)
+ # Run NN
+ COILS_raw, HOTLOOPS_raw, REM465_raw = JensenNet(sequence)
+ # Run Savitzky-Golay
+ REM465_smooth = SavitzkyGolay(smooth_frame,0,REM465_raw)
+ COILS_smooth = SavitzkyGolay(smooth_frame,0,COILS_raw)
+ HOTLOOPS_smooth = SavitzkyGolay(smooth_frame,0,HOTLOOPS_raw)
+ if mode == 'default':
+ sys.stdout.write('> '+cur_record.title+'_COILS ')
+ reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
+ sys.stdout.write('> '+cur_record.title+'_REM465 ')
+ reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
+ sys.stdout.write('> '+cur_record.title+'_HOTLOOPS ')
+ reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
+ sys.stdout.write('\n')
+ elif mode == 'scores':
+ sys.stdout.write('> '+cur_record.title+'\n')
+ sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
+ for i in range(len(REM465_smooth)):
+ sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
+ else:
+ sys.stderr.write('Wrong mode given: '+mode+'\n')
+ raise SystemExit
+ except AttributeError:
+ break
+ return
+
+runDisEMBLpipeline()
--- /dev/null
+#!/usr/local/bin/python
+# Copyright (C) 2004 Rune Linding & Lars Juhl Jensen - EMBL
+# The DisEMBL is licensed under the GPL license
+# (http://www.opensource.org/licenses/gpl-license.php)
+# DisEMBL pipeline
+
+from string import *
+from sys import argv
+from Bio import File
+from Bio import Fasta
+import fpformat
+import sys
+import tempfile
+import os
+from os import system,popen3
+
+# change these to the correct paths
+NN_bin = '/PATH/DisEMBL-1.4/disembl'
+SG_bin = '/PATH/DisEMBL-1.4/sav_gol'
+
+def JensenNet(sequence):
+ outFile = tempfile.mktemp()
+ inFile= tempfile.mktemp()
+ open(inFile,'w').write(sequence+'\n')
+ system(NN_bin + '< ' + inFile +' > ' + outFile)
+ REM465 = []
+ COILS = []
+ HOTLOOPS = []
+ resultsFile = open(outFile,'r')
+ results = resultsFile.readlines()
+ resultsFile.close()
+ for result in results:
+ coil = float(fpformat.fix(split(result)[0],6))
+ COILS.append(coil)
+ hotloop = float(fpformat.fix(split(result)[1],6))
+ HOTLOOPS.append(hotloop)
+ rem465 = float(fpformat.fix(split(result)[2],6))
+ REM465.append(rem465)
+ os.remove(inFile)
+ os.remove(outFile)
+ return COILS, HOTLOOPS, REM465
+
+
+def SavitzkyGolay(window,derivative,datalist):
+ if len(datalist) < 2*window:
+ window = len(datalist)/2
+ elif window == 0:
+ window = 1
+ stdin, stdout, stderr = popen3(SG_bin + ' -V0 -D' + str(derivative) + ' -n' + str(window)+','+str(window))
+ for data in datalist:
+ stdin.write(`data`+'\n')
+ try:
+ stdin.close()
+ except:
+ print stderr.readlines()
+ results = stdout.readlines()
+ stdout.close()
+ SG_results = []
+ for result in results:
+ f = float(fpformat.fix(result,6))
+ if f < 0:
+ SG_results.append(0)
+ else:
+ SG_results.append(f)
+ return SG_results
+
+def getSlices(NNdata, fold, join_frame, peak_frame, expect_val):
+ slices = []
+ inSlice = 0
+ for i in range(len(NNdata)):
+ if inSlice:
+ if NNdata[i] < expect_val:
+ if maxSlice >= fold*expect_val:
+ slices.append([beginSlice, endSlice])
+ inSlice = 0
+ else:
+ endSlice += 1
+ if NNdata[i] > maxSlice:
+ maxSlice = NNdata[i]
+ elif NNdata[i] >= expect_val:
+ beginSlice = i
+ endSlice = i
+ inSlice = 1
+ maxSlice = NNdata[i]
+ if inSlice and maxSlice >= fold*expect_val:
+ slices.append([beginSlice, endSlice])
+
+ i = 0
+ while i < len(slices):
+ if i+1 < len(slices) and slices[i+1][0]-slices[i][1] <= join_frame:
+ slices[i] = [ slices[i][0], slices[i+1][1] ]
+ del slices[i+1]
+ elif slices[i][1]-slices[i][0]+1 < peak_frame:
+ del slices[i]
+ else:
+ i += 1
+ return slices
+
+
+def reportSlicesTXT(slices, sequence):
+ if slices == []:
+ s = lower(sequence)
+ else:
+ if slices[0][0] > 0:
+ s = lower(sequence[0:slices[0][0]])
+ else:
+ s = ''
+ for i in range(len(slices)):
+ if i > 0:
+ sys.stdout.write(', ')
+ sys.stdout.write( str(slices[i][0]+1) + '-' + str(slices[i][1]+1) )
+ s = s + upper(sequence[slices[i][0]:(slices[i][1]+1)])
+ if i < len(slices)-1:
+ s = s + lower(sequence[(slices[i][1]+1):(slices[i+1][0])])
+ elif slices[i][1] < len(sequence)-1:
+ s = s + lower(sequence[(slices[i][1]+1):(len(sequence))])
+ print ''
+ print s
+
+
+
+def runDisEMBLpipeline():
+ try:
+ smooth_frame = int(sys.argv[1])
+ peak_frame = int(sys.argv[2])
+ join_frame = int(sys.argv[3])
+ fold_coils = float(sys.argv[4])
+ fold_hotloops = float(sys.argv[5])
+ fold_rem465 = float(sys.argv[6])
+ file = str(sys.argv[7])
+ try:
+ mode = sys.argv[8]
+ except:
+ mode = 'default'
+ except:
+ print '\nDisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file [mode]\n'
+ print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file'
+ print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB seperated format'
+ raise SystemExit
+ db = open(file,'r')
+ parser = Fasta.RecordParser()
+ iterator = Fasta.Iterator(db,parser)
+ print ' ____ _ _____ __ __ ____ _ _ _ _'
+ print '| _ \(_)___| ____| \/ | __ )| | / || || |'
+ print '| | | | / __| _| | |\/| | _ \| | | || || |_'
+ print '| |_| | \__ \ |___| | | | |_) | |___ | ||__ _|'
+ print '|____/|_|___/_____|_| |_|____/|_____| |_(_) |_|'
+ print '# Copyright (C) 2004 - Rune Linding & Lars Juhl Jensen '
+ print '# EMBL Biocomputing Unit - Heidelberg - Germany '
+ print '#'
+ while 1:
+ try:
+ cur_record = iterator.next()
+ sequence = upper(cur_record.sequence)
+ # Run NN
+ COILS_raw, HOTLOOPS_raw, REM465_raw = JensenNet(sequence)
+ # Run Savitzky-Golay
+ REM465_smooth = SavitzkyGolay(smooth_frame,0,REM465_raw)
+ COILS_smooth = SavitzkyGolay(smooth_frame,0,COILS_raw)
+ HOTLOOPS_smooth = SavitzkyGolay(smooth_frame,0,HOTLOOPS_raw)
+ if mode == 'default':
+ sys.stdout.write('> '+cur_record.title+'_COILS ')
+ reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
+ sys.stdout.write('> '+cur_record.title+'_REM465 ')
+ reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
+ sys.stdout.write('> '+cur_record.title+'_HOTLOOPS ')
+ reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
+ sys.stdout.write('\n')
+ elif mode == 'scores':
+ sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
+ for i in range(len(REM465_smooth)):
+ sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
+ else:
+ sys.stderr.write('Wrong mode given: '+mode+'\n')
+ raise SystemExit
+ except AttributeError:
+ break
+ return
+
+runDisEMBLpipeline()
--- /dev/null
+Quick Install Guide:
+
+1) Install Python 2.2+ from http://www.python.org
+2) Install Biopython.org from http://www/biopython.org
+3) Download and compile the savgol module in TISEAN, http://lists.mpipks-dresden.mpg.de/~tisean/TISEAN_2.1/index.html
+ - just compile the full package and copy the module from TISEAN-2.1/source_c/sav_gol to the DisEMBL directory.
+
+4) Compile disembl's neural network (gcc -O3 disembl.c -o disembl)
+5) Set correct paths to the neural net binary and savgol at the top of the script:
+ from /PATH/DisEMBL-1.x to the correct path
+
+Now you should be able to parse in a sequence file containing multiple fasta entries...
+just do a "./DisEMBL.py 8 8 4 1.2 1.4 1.2 sequence_file" if you want to save the results add " > resultfile.disembl"
+after the command
+
--- /dev/null
+DIsEMBL depends on BioPython and Tisean sav_gol executable
+both has to be installed
+DisEMBL.py script changes:
+move import sys statement up to append Bio python libraries path
+change path to python interpreter
+Comment out file argument read data from stdin instead
+was:
+ file = str(sys.argv[7])
+ db = open(file,'r')
+become:
+# file = str(sys.argv[7])
+ db = sys.stdin
+
+Header
+ print ' ____ _ _____ __ __ ____ _ _ _ _'
+ print '| _ \(_)___| ____| \/ | __ )| | / || || |'
+ print '| | | | / __| _| | |\/| | _ \| | | || || |_'
+ print '| |_| | \__ \ |___| | | | |_) | |___ | ||__ _|'
+ print '|____/|_|___/_____|_| |_|____/|_____| |_(_) |_|'
+ print '# Copyright (C) 2004 - Rune Linding & Lars Juhl Jensen '
+ print '# EMBL Biocomputing Unit - Heidelberg - Germany '
+ print ''
+removed to facilitate parsing
--- /dev/null
+The GNU General Public License (GPL)
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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+Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
+To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
+ one line to give the program's name and a brief idea of what it does.
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
+ This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest
+ in the program `Gnomovision' (which makes passes at compilers)
+ written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License.
--- /dev/null
+float const b41_1[(na*41+1)*5+(5+1)*2] = {
+ -0.29703, -0.13434, -0.00089, 0.24669, 0.17172,
+ -0.12640, 0.28457, -0.41355, -0.41871, -0.04025,
+ -0.36689, 0.38753, 0.10060, -0.31521, 0.28160,
+ -0.08703, 0.18120, -0.05225, -0.20045, 0.30254,
+ 0.51176, 0.07855, 0.15753, -0.10894, 0.00512,
+ 0.04612, -0.07720, 0.25057, -0.23093, -0.48657,
+ 0.18707, -0.25023, -0.30363, 0.40785, -0.04128,
+ -0.05314, -0.12819, 0.21573, 0.05552, 0.06068,
+ -0.00206, 0.42629, 0.09881, -0.05796, -0.51255,
+ 0.05595, 0.07914, -0.49773, -0.24440, 0.01912,
+ 0.31516, 0.17460, 0.05195, -0.03982, 0.12648,
+ -0.20893, -0.50688, 0.09315, 0.31890, 0.65921,
+ -0.10246, 0.47419, 0.11293, -0.03158, -0.48387,
+ -0.30309, -0.01726, 0.08578, 0.16205, 0.02433,
+ -0.05833, -0.17001, -0.03779, -0.16581, 0.37351,
+ 0.24897, -0.03355, -0.28998, 0.17541, 0.58996,
+ 0.30361, -0.32262, 0.23236, 0.06954, 0.22215,
+ -0.18216, -0.16232, -0.04761, 0.23932, -0.22046,
+ -0.17055, 0.00993, 0.00594, -0.10511, -0.53607,
+ 0.16146, 0.19542, 0.21550, -0.05497, -0.18711,
+ 0.44439, -0.32479, -0.01222, 0.53190, 0.34781,
+ 0.03974, -0.00517, 0.13599, 0.12441, -0.01250,
+ -0.29264, -0.08880, -0.05335, -0.13730, -0.04184,
+ -0.04473, 0.10503, -0.16847, -0.15269, -0.21123,
+ -0.14881, 0.34813, 0.07288, -0.12738, 0.40264,
+ 0.45243, 0.14560, -0.09750, -0.06193, 0.02937,
+ 0.00235, -0.05248, -0.39234, -0.34327, -0.19058,
+ -0.14630, -0.28009, -0.08845, 0.22354, 0.24956,
+ 0.12640, 0.16055, 0.48099, -0.30909, -0.21943,
+ 0.42208, 0.35639, 0.05453, -0.07906, -0.23803,
+ 0.12298, -0.03800, 0.01246, -0.26236, -0.34449,
+ -0.02028, -0.17017, -0.17643, 0.11104, 0.24805,
+ -0.18783, -0.23031, -0.27348, 0.40693, -0.06846,
+ 0.23272, 0.40810, 0.34393, -0.01512, 0.09647,
+ 0.25138, -0.08099, -0.28706, -0.23580, 0.03830,
+ -0.14416, 0.11333, -0.12267, -0.08777, 0.26386,
+ -0.02386, -0.22048, -0.12158, -0.31674, -0.10961,
+ 0.01989, -0.05266, 0.11199, 0.48158, 0.04981,
+ -0.06582, 0.38695, -0.21105, -0.29411, 0.33717,
+ 0.03121, -0.44151, 0.10401, 0.06908, -0.90278,
+ -0.13311, -0.05984, -0.21376, 0.12197, 0.13879,
+ 0.68815, 0.09771, -0.20705, 0.02441, 0.24455,
+ 0.16760, -0.14779, 0.07776, -0.16713, -0.05336,
+ 0.11102, -0.55104, -0.16209, -0.15366, -0.25187,
+ -0.06178, 0.27030, 0.04798, 0.00106, 0.09581,
+ 0.31758, 0.31494, -0.12988, 0.33168, 0.08137,
+ 0.37689, 0.33820, -0.37713, 0.54574, -0.33671,
+ -0.14157, -0.15249, 0.07926, 0.10309, 0.00684,
+ -0.16167, -0.28201, -0.34016, 0.21629, -0.04400,
+ -0.16580, -0.09166, 0.57058, 0.50344, 0.30094,
+ -0.19629, 0.21240, 0.25715, -0.31206, 0.12573,
+ 0.21788, -0.04751, -0.04504, 0.02488, -0.28085,
+ -0.18010, 0.04671, -0.03442, -0.46312, 0.03827,
+ 0.38064, -0.18651, -0.00560, 0.10273, 0.09377,
+ 0.21045, 0.41624, 0.00753, -0.16012, -0.04537,
+ 0.31676, 0.19735, 0.38303, -0.27950, -0.02758,
+ -0.09708, -0.16813, 0.33289, -0.01370, -0.17034,
+ 0.07751, 0.06912, 0.08945, -0.12518, -0.00193,
+ -0.03312, -0.12845, 0.20432, 0.05937, 0.08113,
+ -0.51567, 0.35054, -0.09066, 0.04627, -0.40744,
+ -0.09585, -0.05910, -0.47208, 0.52901, 0.00868,
+ -0.04684, 0.02158, -0.18332, 0.03820, 0.30406,
+ 0.04360, -0.19538, 0.23847, 0.28568, 0.28710,
+ 0.01874, 0.07100, 0.47150, -0.11903, -0.39694,
+ -0.14350, 0.04125, -0.09338, -0.29821, -0.12153,
+ 0.37342, -0.13326, -0.13662, -0.47655, 0.24079,
+ -0.18632, 0.29288, 0.40187, 0.22415, -0.03005,
+ 0.17948, -0.11697, -0.28801, 0.05883, 0.28485,
+ -0.02966, -0.08767, -0.23880, 0.05614, 0.04411,
+ 0.00282, -0.09482, -0.31261, 0.33666, 0.05873,
+ 0.24706, -0.00638, 0.17299, 0.23925, -0.20720,
+ 0.00531, 0.28754, -0.39174, 0.04133, 0.14507,
+ 0.30356, 0.05017, 0.01089, -0.31736, 0.03387,
+ -0.28454, -0.03005, -0.14338, -0.41516, 0.34182,
+ -0.01637, 0.13765, 0.34349, -0.31849, 0.13862,
+ 0.20953, 0.29351, 0.35770, -0.16074, 0.25756,
+ 0.00786, 0.11964, -0.26419, 0.09305, -0.51649,
+ 0.16750, -0.36321, 0.24426, 0.37660, -0.10051,
+ 0.09379, -0.21341, 0.25576, -0.13297, -0.19244,
+ 0.28681, 0.22701, -0.15005, 0.48230, 0.11152,
+ -0.23938, -0.05498, 0.13741, -0.04310, -0.38470,
+ -0.35676, 0.03026, -0.18085, 0.07820, -0.14923,
+ -0.20375, 0.25006, -0.13824, 0.25214, 0.36632,
+ 0.12550, -0.02791, 0.02742, 0.36854, 0.27378,
+ -0.18080, -0.10355, -0.31695, 0.31792, -0.17909,
+ 0.18095, -0.21215, -0.05365, -0.55286, -0.21217,
+ -0.03872, -0.27126, 0.08966, -0.00107, -0.38721,
+ 0.01048, 0.26133, -0.10945, 0.73803, 0.59833,
+ 0.10000, -0.13069, -0.05533, 0.46419, -0.22697,
+ -0.41538, -0.17663, -0.10924, 0.18632, -0.08699,
+ 0.17652, 0.29401, 0.33956, 0.45985, 0.48710,
+ -0.30380, -0.31473, 0.05682, 0.19624, 0.01269,
+ 0.27908, 0.11877, 0.14762, -0.20683, -0.02825,
+ -0.14090, -0.38098, 0.03643, -0.37834, -0.00756,
+ 0.00661, 0.04306, 0.12133, -0.07186, 0.44867,
+ 0.37723, -0.31198, 0.09170, -0.49585, -0.16521,
+ -0.21124, 0.40080, 0.25765, -0.31252, 0.20919,
+ -0.26212, -0.48041, -0.29582, -0.31318, -0.07774,
+ 0.04704, -0.06547, 0.06513, -0.08548, 0.01347,
+ 0.33669, 0.53601, -0.41991, 0.08203, 0.39378,
+ 0.41603, 0.11175, 0.33968, 0.21925, 0.08257,
+ 0.27431, -0.20318, -0.27955, -0.31656, 0.16575,
+ -0.29638, -0.09682, -0.18167, 0.31903, 0.06207,
+ -0.12304, 0.31198, 0.26462, 0.17076, -0.57613,
+ -0.00615, 0.20623, -0.02082, 0.26293, -0.11470,
+ -0.00946, 0.22755, 0.65298, -0.09990, -0.42741,
+ -0.51791, -0.54358, 0.23005, 0.26455, 0.19829,
+ -0.05226, -0.08056, 0.31663, 0.13829, -0.07195,
+ 0.25459, -0.21799, -0.10467, 0.05154, -0.02221,
+ 0.05655, 0.30488, -0.20427, 0.14651, -0.12470,
+ -0.08049, 0.17261, -0.29193, 0.07764, 0.10424,
+ -0.18572, -0.00795, -0.06625, 0.55725, 0.24007,
+ -0.14598, 0.13294, 0.13591, -0.12042, 0.22548,
+ -0.05724, 0.17402, -0.24493, 0.01434, 0.17777,
+ -0.03441, 0.00184, 0.00247, -0.14036, -0.09533,
+ -0.33326, 0.36379, 0.23831, -0.26026, 0.50365,
+ 0.32179, 0.09782, -0.15997, -0.09686, -0.11109,
+ -0.27198, 0.37907, 0.05010, 0.02037, 0.40385,
+ 0.34847, -0.14300, -0.47130, -0.38132, 0.01269,
+ 0.12159, -0.07519, -0.00564, 0.00362, -0.11937,
+ 0.11826, 0.36087, -0.12084, 0.03370, 0.35778,
+ 0.29940, -0.00499, -0.13806, 0.08882, -0.30465,
+ -0.04701, -0.05679, -0.05526, -0.27838, -0.06587,
+ 0.02699, 0.06553, 0.41748, 0.09355, 0.03453,
+ 0.30788, 0.43614, -0.17021, -0.20911, -0.01208,
+ 0.18969, 0.43112, -0.52998, 0.02395, 0.09377,
+ 0.04742, 0.30326, 0.34885, -0.20092, -0.15505,
+ 0.01057, 0.09158, 0.14150, 0.20401, 0.15735,
+ -0.27254, -0.17825, 0.22034, -0.15437, 0.06560,
+ 0.03425, -0.13229, 0.22267, -0.08301, -0.10273,
+ 0.17700, 0.08816, -0.08245, -0.03834, 0.29906,
+ -0.07628, -0.09381, -0.14285, -0.27234, -0.26100,
+ 0.03772, 0.02282, -0.02565, 0.49519, 0.19892,
+ -0.30563, -0.03235, -0.00998, 0.07913, -0.21996,
+ -0.17124, -0.20341, 0.10241, -0.26598, -0.31961,
+ 0.23022, -0.05753, -0.10501, -0.15638, 0.02876,
+ 0.09416, -0.24870, -0.82465, -0.11489, 0.47825,
+ 0.39887, 0.17489, 0.42622, -0.00941, -0.06603,
+ 0.32226, 0.23349, -0.19598, -0.09391, -0.08981,
+ 0.20145, 0.04817, -0.13369, 0.19339, -0.05280,
+ 0.17043, -0.11347, 0.47404, -0.32680, -0.41933,
+ 0.13479, 0.39799, 0.13379, 0.09678, -0.23587,
+ -0.33173, -0.40765, -0.01244, 0.11291, 0.00581,
+ -0.42898, 0.44661, -0.06290, 0.11391, 0.15084,
+ -0.08929, -0.19507, -0.37237, -0.05820, 0.10300,
+ -0.13502, 0.02282, -0.00957, -0.05961, 0.19113,
+ 0.16372, -0.15751, 0.15255, -0.20412, -0.22181,
+ -0.05243, -0.18660, -0.13710, -0.20665, -0.31857,
+ 0.49055, -0.16703, -0.00397, -0.21865, -0.05235,
+ -0.20337, -0.07628, 0.23833, 0.15984, -0.28125,
+ 0.63913, -0.00356, -0.21989, 0.02263, 0.15555,
+ -0.42727, 0.32315, 0.07211, 0.11042, -0.00918,
+ -0.39737, 0.22699, -0.18146, -0.28120, 0.22822,
+ 0.00361, -0.12587, -0.08056, 0.07046, 0.16431,
+ -0.26270, 0.07388, 0.27763, -0.32238, -0.16227,
+ 0.19668, -0.19145, -0.25839, 0.02433, 0.26835,
+ -0.09379, -0.23478, 0.14542, 0.10088, -0.31045,
+ -0.18190, -0.31226, 0.42979, -0.12639, 0.38302,
+ 0.42961, -0.22830, 0.13842, 0.05181, -0.39048,
+ 0.45971, -0.38577, -0.25297, 0.10239, -0.06597,
+ 0.29098, 0.00055, -0.01608, 0.36703, 0.19608,
+ -0.17012, 0.04159, 0.14647, -0.31927, -0.08507,
+ 0.04203, -0.37280, 0.23340, 0.37252, 0.13664,
+ -0.29348, 0.53990, -0.36884, 0.07339, -0.35048,
+ -0.18672, -0.19729, -0.07321, -0.06125, -0.21259,
+ -0.08597, 0.17766, -0.15580, 0.38554, 0.02327,
+ 0.07372, 0.00528, 0.01225, 0.08905, 0.49190,
+ -0.07434, 0.30945, 0.47423, -0.08920, -0.24339,
+ -0.00801, 0.17422, 0.28615, -0.29375, -0.30545,
+ 0.11216, -0.11257, -0.33044, -0.42197, 0.00977,
+ -0.10676, -0.08897, 0.39932, 0.29283, 0.55732,
+ -0.02983, -0.12189, -0.08284, -0.02053, 0.03098,
+ -0.01880, 0.27775, 0.28738, -0.04390, 0.11646,
+ 0.28806, -0.15313, 0.55950, -0.10281, 0.17142,
+ -0.31736, 0.57226, 0.20548, -0.19414, 0.30391,
+ -0.05993, -0.02400, -0.66001, -0.14992, 0.20067,
+ 0.00084, 0.06125, -0.36342, 0.44027, -0.05742,
+ 0.30579, -0.17595, -0.78348, 0.52673, 0.00715,
+ 0.16886, -0.36255, -0.00855, 0.23969, 0.44678,
+ -0.09227, 0.34922, 0.20793, -0.31956, -0.49002,
+ 0.09774, -0.14279, -0.53110, 0.26732, 0.39524,
+ 0.15204, -0.27919, -0.10703, -0.64154, 0.05794,
+ 0.15824, -0.30993, -0.15812, 0.15581, 0.14554,
+ 0.08446, -0.15329, 0.08852, -0.07682, 0.12952,
+ 0.27166, 0.25380, -0.16221, -0.22736, 0.63193,
+ 0.36273, -0.21236, 0.25317, 0.02738, -0.43178,
+ 0.51836, 0.58839, -0.09174, -0.45411, -0.05341,
+ 0.23439, 0.16458, -0.40664, -0.17641, 0.31017,
+ -0.69577, -0.06896, 0.60300, -0.33255, 0.18201,
+ 0.57087, 0.27507, 0.08788, 0.19791, 0.16324,
+ -0.04393, -0.32148, 0.61932, 0.47895, -0.23611,
+ 0.24028, -0.91614, 0.14044, -0.69056, -0.04830,
+ 0.15080, -0.50793, 0.22447, 0.35463, 0.01003,
+ 0.05831, 0.23022, 0.22209, -0.48251, 0.36108,
+ -0.22554, 0.22273, -0.40612, 0.31061, 0.36282,
+ 0.41025, 0.34469, 0.20449, 0.47814, -0.89449,
+ -0.25466, 0.57467, -0.22232, -0.01886, 0.13477,
+ 0.05642, -0.52932, -0.15586, 0.07187, -0.38556,
+ -0.38560, -0.30138, 0.40868, -0.38415, 0.14508,
+ 0.46744, -0.49651, 0.62485, 0.34577, 0.26847,
+ 0.21625, 0.38198, 0.01865, -0.40479, 0.20223,
+ -0.11050, -0.21992, 0.36449, -0.39736, -0.29697,
+ 0.01333, -0.08588, -0.35132, -0.04228, -0.05220,
+ 0.62692, 0.45425, -0.52692, 0.04384, -0.01150,
+ 0.06239, -0.30409, -0.04624, -0.18378, -0.07252,
+ 0.16169, 0.89393, 0.34616, -0.22557, -0.31676,
+ 0.10704, -0.00965, -0.29196, -0.38503, 0.25493,
+ -0.25547, 0.16854, 0.50098, -0.48492, 0.13881,
+ -0.13639, 0.29992, -0.03112, -0.13312, -0.17095,
+ 0.03963, 0.28458, 0.37485, 0.20503, -0.02667,
+ 0.21321, 0.13071, 0.48536, 0.50200, 0.23751,
+ 0.43728, 0.08488, -0.31915, 0.37647, -0.40846,
+ 0.33857, -0.13148, -0.28617, -0.86236, -0.42299,
+ 0.24282, -0.36263, 0.61434, 0.09286, -0.25878,
+ -0.37234, -0.05552, -0.10305, -0.70496, -0.04173,
+ 0.63880, 0.40827, 0.26637, 0.44720, 0.19049,
+ -0.31479, -0.17099, 0.04171, -0.12336, -1.01230,
+ -0.45993, 0.09814, 0.03198, 0.54348, 0.39356,
+ 0.08890, 0.06453, -0.18793, 0.04784, -0.32488,
+ -0.04588, 0.62735, 0.10408, -0.46103, 0.22818,
+ 0.53888, 0.12524, -0.37453, -0.10464, -0.04854,
+ -0.36498, -0.09493, 0.32648, -0.11892, 0.19040,
+ 0.29352, 0.09025, -0.46333, 0.25144, 0.49457,
+ -0.35030, -0.15093, 0.08457, -0.56934, -0.15254,
+ -0.14685, 0.49053, -0.50065, 0.34083, 0.70508,
+ -0.49721, -0.25336, -0.25462, 0.13926, 0.57150,
+ -0.14474, 0.49892, 0.17897, -0.46887, 0.08521,
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+ -0.07032, -0.06079, -0.03405, 0.35675, 0.34013,
+ 0.47073, -0.07420, 0.46126, -0.29493, 0.17587,
+ -0.04656, -0.73373, -0.02203, -0.23393, 0.18838,
+ -0.24482, -0.57515, 0.44205, -0.03450, -0.28428,
+ -0.00414, 0.51602, -0.10300, -0.17425, -0.12309,
+ 0.14037, 0.08384, 0.08490, 0.08717, -0.27308,
+ 0.07928, -0.15335, -0.61239, -0.06154, 0.31487,
+ 0.25775, -0.34665, -0.20261, 0.02472, -0.07941,
+ -0.12969, 0.21011, -0.18429, -0.02880, -0.27409,
+ 0.20750, 0.34916, 0.39576, 0.02792, 0.38742,
+ -0.21540, -0.20034, 0.29985, -0.09112, -0.22887,
+ -0.29856, -0.17645, 0.30596, -0.06481, -0.39783,
+ 0.13014, -0.45788, 0.06475, -0.16628, 0.16943,
+ 0.04143, 0.18596, 0.26532, 0.30151, -0.12033,
+ 0.37148, -0.01523, 0.46843, -0.07162, -0.45491,
+ 0.00754, 0.01362, -0.22120, -0.81586, 0.44704,
+ -0.08377, 0.08669, -0.23392, 0.29562, -0.33869,
+ 0.01875, -0.36385, 0.23329, 0.22297, 0.40848,
+ -0.29439, 0.49203, 0.30255, 0.30078, 0.07910,
+ -0.55266, 0.16946, 0.25615, -0.26146, 0.02636,
+ -0.27972, 0.09615, -0.53863, 0.10000, 0.34748,
+ 0.04878, -0.20581, 0.05790, 0.50341, 0.27255,
+ 0.24055, 0.04219, 0.56398, 0.29580, -0.06027,
+ -0.24802, -0.70132, -0.44343, 0.36987, -0.30498,
+ -0.43427, 0.29663, -0.20866, -0.53654, -0.29302,
+ 0.02706, -0.54393, -0.07388, 0.27489, 0.63800,
+ 0.33982, 0.48394, 0.42291, 0.39022, -0.79547,
+ -0.00816, 0.09485, -0.03450, -0.21744, 0.36283,
+ -0.32825, 0.33819, -0.02373, -0.19349, -0.34540,
+ -0.23920, 0.15995, 0.07173, -0.35890, 0.64477,
+ 0.41723, 0.92831, 0.42693, -0.03451, 0.40039,
+ -0.17444, -0.00769, 0.28038, -0.32256, -0.58301,
+ -0.07077, 0.31460, 0.29257, -0.47005, 0.29126,
+ -0.62793, -0.41402, -0.36897, -0.69226, -0.29680,
+ 0.46033, 0.82298, 0.74384, 0.17963, -0.03902,
+ -0.10275, -0.12306, 0.15662, -0.01359, 0.03196,
+ -0.49371, -0.06366, 0.14059, -0.21726, 0.12391,
+ 0.20122, -0.11809, -0.18365, 0.32669, -0.21591,
+ -0.61273, 0.21757, 0.12090, 0.47007, 0.53434,
+ 0.10964, -0.13331, -0.11278, 0.28287, 0.41330,
+ -0.25254, -0.35834, 0.13689, 0.20063, 0.20634,
+ 0.16767, 0.12627, 0.12736, -0.10164, -0.36732,
+ 0.14954, -0.14393, 0.09359, 0.06770, 0.41996,
+ 0.10473, -0.52194, -0.01080, -0.42762, 0.30096,
+ 0.38349, -0.00616, 0.24852, 0.00133, -0.20940,
+ 0.09939, -0.01352, 0.02264, 0.03391, -0.39316,
+ -0.04915, -0.28125, -0.08552, 0.19614, 0.36848,
+ -0.28165, 0.43271, 0.12083, 0.09037, -0.20678,
+ 0.19853, 0.42084, -0.25008, 0.05828, -0.03227,
+ -0.19581, 0.11348, 0.19295, 0.29029, -0.75371,
+ -0.11983, 0.45704, -0.06244, -0.19271, 0.24915,
+ 0.28220, 0.27632, -0.00335, 0.31556, -0.08854,
+ 0.00564, -0.07373, 0.36077, -0.39772, -0.11366,
+ 0.34036, -0.03030, -0.11391, 0.03791, 0.20187,
+ -0.11577, -0.13831, 0.39408, -0.15903, -0.44516,
+ 0.13439, 0.42726, 0.23770, -0.46414, -0.04823,
+ -0.19373, -0.59551, 0.26464, -0.23662, -0.03140,
+ 0.19021, 0.32647, 0.09926, -0.60739, -0.08208,
+ 0.71170, -0.33633, 0.01450, 0.31337, -0.29751,
+ 0.50229, 0.00984, 0.43942, 0.19560, -0.33916,
+ 0.17742, -0.39608, 0.16012, 0.27366, -0.07162,
+ -0.23371, 0.31595, 0.40123, -0.25300, -0.63377,
+ -0.05675, 0.16991, 0.11109, -0.33694, 0.28091,
+ -0.47306, -0.09165, -0.15141, 0.08107, 0.58800,
+ 0.43958, 0.31624, 0.22276, 0.06827, 0.16579,
+ 0.38198, -0.09929, -0.51226, 0.18413, -0.55109,
+ -0.33888, -0.37903, 0.04461, -0.10712, 0.35659,
+ -0.40849, 0.26539, -0.16886, 0.21690, 0.25568,
+ 0.32876, -0.08062, 0.13046, 0.05099, -0.17504,
+ 0.44855, 0.03920, -0.86417, 0.34598, -0.22071,
+ 0.04100, 0.29622, -0.10517, -0.26245, -0.47411,
+ -0.15638, 0.33324, 0.32573, 0.36521, -0.16941,
+ 0.41599, -0.22001, -0.33018, -0.08885, -0.48766,
+ -0.11620, 0.58639, 0.57765, -0.43022, -0.24448,
+ 0.20323, -0.29563, -0.15782, -0.06465, 0.45009,
+ -0.51516, -0.66863, -0.38935, 0.44805, -0.01240,
+ 0.36270, 0.07805, -0.29925, -0.19903, 0.02297,
+ 0.48041, -0.08225, 0.21582, 0.05080, 0.28592,
+ 0.06492, -0.11968, -0.31518, 0.55309, -0.16118,
+ -0.74940, -0.33968, -0.05555, 0.06931, 0.34048,
+ -0.98161, 0.16837, 0.20945, -0.12284, 0.54555,
+ 0.10859, 0.13975, -0.15366, 0.44638, 0.18798,
+ 0.26260, -0.03126, 0.31800, -0.47438, -0.08532,
+ -0.04042, -0.24980, -0.19664, -0.01129, -0.01179,
+ 0.23903, 0.04278, -0.32776, 0.33933, 0.39818,
+ 0.28170, 0.32158, -0.28463, -0.34521, 0.12313,
+ 0.14012, 0.21016, -0.16786, 0.06826, -0.29886,
+ 0.01906, 0.43691, -0.14256, -0.53746, 0.00864,
+ 0.00375, 0.32476, -0.01175, 0.20497, 0.48534,
+ -0.53354, -0.15030, 0.21942, -0.04339, -0.23888,
+ 0.21150, 0.17629, -0.87038, 0.26070, -0.35604,
+ -0.01123, -0.04883, 0.37242, 0.00812, -0.08139,
+ -0.02675, 0.07918, 0.33763, -0.54004, 0.02538,
+ -0.18637, -0.13448, 0.01662, 0.23140, -0.09910,
+ -0.44448, 0.04138, 0.12548, 0.25743, 0.13599,
+ -0.19818, -0.23508, -0.48893, 0.38886, 0.30650,
+ 0.54025, 0.11834, 0.37831, -0.05830, -0.20087,
+ 0.29875, 0.14158, -0.39064, 0.15569, 0.07668,
+ 0.37171, -0.00206, 0.27792, 0.06837, 0.00953,
+ 0.08617, -0.23379, -0.36206, 0.01209, -0.01034,
+ -0.46449, 0.09270, 0.46358, 0.20450, -0.07183,
+ -0.41592, 0.24431, 0.17805, -0.38954, 0.31235,
+ 0.11246, 0.91290, 0.46316, 0.46365, 0.16474,
+ -0.29260, -0.03866, -0.44042, -0.38158, -0.35263,
+ 0.05331, 0.32309, -0.46367, -0.10512, 0.37228,
+ 2.71244, -4.20403, 2.09935, -1.52759, -3.40162,
+ -1.22824, -2.71546, 4.20243, -2.10157, 1.52387,
+ 3.39937, 1.23391,
+};
+
+float const b41_2[(na*41+1)*5+(5+1)*2] = {
+ -0.29317, -0.25277, 0.02489, 0.03480, 0.32139,
+ -0.08091, 0.15299, -0.45546, -0.29805, -0.35356,
+ -0.05184, 0.26334, 0.40993, -0.12664, 0.11353,
+ 0.03973, 0.24841, -0.29297, -0.07560, 0.37723,
+ 0.12844, 0.00548, 0.25269, -0.09812, 0.03864,
+ 0.13753, 0.08928, 0.09921, -0.31262, -0.38877,
+ 0.26445, -0.26567, -0.15278, 0.48404, 0.05205,
+ -0.17168, -0.02501, 0.03927, -0.39124, 0.17931,
+ 0.11470, 0.12784, 0.07053, 0.17922, -0.42723,
+ 0.18820, 0.31378, -0.68181, -0.27923, -0.16417,
+ 0.30594, 0.07684, 0.31597, 0.01654, 0.03770,
+ -0.16199, -0.41031, 0.17324, 0.31827, 0.46233,
+ 0.10769, 0.16208, -0.29765, -0.42169, -0.28622,
+ -0.17756, 0.06044, 0.11614, 0.21762, 0.03234,
+ -0.20803, 0.10604, 0.08943, 0.06792, 0.46271,
+ 0.26255, 0.22499, -0.12578, 0.07888, 0.37995,
+ 0.09112, -0.44709, 0.15316, -0.38989, -0.01003,
+ -0.15201, -0.19634, -0.26741, 0.28946, 0.21564,
+ -0.07405, 0.10379, 0.00861, 0.02651, -0.54261,
+ 0.07653, 0.49245, 0.38206, 0.01955, -0.16491,
+ 0.44084, -0.32867, -0.02010, 0.18181, -0.20840,
+ -0.22002, 0.03861, 0.12541, 0.08851, 0.05546,
+ 0.07390, 0.13752, -0.01757, 0.08114, -0.26381,
+ -0.04327, -0.01307, -0.16191, 0.08089, -0.22126,
+ -0.23582, 0.27655, 0.12579, -0.02772, 0.23434,
+ -0.05134, -0.15798, 0.14726, -0.04327, -0.00711,
+ 0.12488, 0.04324, -0.32780, -0.45426, 0.02221,
+ -0.01879, -0.29689, -0.07530, 0.34169, 0.45892,
+ 0.05509, 0.22691, 0.32722, -0.34914, -0.34659,
+ 0.36843, -0.15484, -0.30987, 0.19329, -0.16148,
+ 0.15808, 0.29445, 0.30660, -0.09338, -0.26293,
+ 0.15395, -0.17919, -0.39608, -0.30161, 0.22233,
+ -0.38025, -0.19402, -0.33037, 0.44594, 0.08841,
+ 0.37206, 0.29267, -0.16692, -0.36114, 0.18344,
+ 0.42808, 0.15165, -0.11180, -0.00256, 0.13842,
+ -0.06764, 0.51660, -0.43426, -0.20736, 0.03647,
+ -0.31170, -0.42920, -0.17302, -0.21750, 0.04217,
+ -0.03152, 0.22668, 0.10112, 0.05380, 0.12684,
+ -0.08317, 0.20926, -0.04912, -0.17212, 0.21069,
+ 0.15607, -0.52815, 0.15899, -0.18817, -0.48659,
+ -0.11513, 0.36384, -0.05116, -0.18785, 0.31181,
+ 0.35043, -0.07599, -0.20052, 0.08861, -0.13233,
+ 0.20278, -0.08322, -0.03248, -0.28628, 0.08813,
+ 0.04869, -0.33489, -0.15424, 0.14306, -0.17265,
+ -0.07862, 0.13453, 0.32171, 0.10314, 0.27753,
+ 0.31982, 0.25895, -0.17519, -0.01773, -0.10256,
+ 0.02203, 0.10963, -0.02665, 0.55029, -0.27445,
+ -0.11176, 0.37323, 0.01943, -0.14307, -0.19546,
+ -0.42565, -0.26111, -0.29107, 0.09240, 0.04610,
+ -0.09796, 0.01697, 0.68238, 0.25572, 0.27235,
+ -0.07695, -0.05510, 0.30873, -0.20946, 0.22989,
+ 0.16303, 0.16135, 0.28268, -0.18773, -0.29265,
+ -0.18422, -0.11653, -0.13211, -0.10472, -0.09663,
+ 0.30655, -0.28591, -0.00994, -0.21102, 0.09540,
+ 0.45725, 0.32863, -0.21589, -0.34272, -0.29955,
+ 0.35423, 0.25167, 0.46488, -0.01862, -0.06961,
+ -0.05358, -0.13203, 0.32778, -0.03718, -0.21387,
+ 0.04397, 0.26534, 0.11617, -0.03932, -0.44585,
+ 0.25195, -0.24876, 0.30430, -0.04838, -0.23771,
+ -0.54471, 0.20996, -0.04110, -0.11360, -0.23602,
+ -0.09260, 0.05638, -0.31171, 0.40234, -0.06079,
+ 0.17021, 0.00977, -0.20980, 0.20807, 0.15242,
+ -0.07814, -0.10849, 0.35481, 0.34184, 0.18981,
+ -0.10321, 0.16297, 0.41417, -0.17307, -0.20300,
+ -0.17768, -0.14044, -0.14679, -0.16198, -0.15072,
+ 0.38842, 0.16318, -0.37577, -0.52708, 0.01424,
+ -0.10891, 0.33692, 0.24746, 0.36649, 0.27575,
+ -0.03308, -0.32134, 0.05880, 0.03677, 0.27776,
+ 0.15157, 0.11826, -0.37190, 0.08862, 0.23814,
+ -0.28793, 0.03158, -0.05628, 0.07065, -0.15583,
+ 0.21154, 0.20015, -0.22278, 0.06959, -0.25901,
+ 0.56788, -0.05509, -0.30899, 0.27342, 0.05476,
+ 0.09873, 0.27664, 0.27151, -0.40983, -0.20536,
+ -0.13596, -0.44644, -0.32461, -0.13594, -0.03170,
+ -0.00239, 0.31151, 0.45323, -0.39323, 0.03553,
+ 0.39384, 0.67663, 0.02168, -0.21316, 0.21137,
+ 0.12776, -0.04336, -0.25668, 0.14366, -0.64366,
+ 0.00890, -0.23681, -0.28467, 0.36049, -0.16729,
+ 0.23561, -0.14864, 0.06323, 0.02560, 0.11441,
+ 0.19876, 0.52106, 0.14592, 0.34523, -0.05610,
+ 0.09816, -0.18526, 0.02900, -0.12871, -0.38483,
+ -0.11174, 0.03983, 0.11838, 0.39268, -0.16523,
+ -0.33563, 0.06052, -0.01525, -0.22024, 0.14373,
+ 0.12838, 0.26431, -0.11838, 0.39443, 0.24382,
+ -0.06629, -0.26183, -0.64474, 0.36492, -0.02375,
+ -0.36022, -0.13421, -0.35170, -0.32473, -0.11874,
+ 0.05984, -0.25137, 0.24998, 0.20029, -0.29300,
+ -0.05691, 0.44805, -0.01038, 0.63806, 0.44123,
+ 0.10000, 0.13941, -0.27944, -0.08353, -0.04800,
+ 0.02357, -0.19950, -0.35904, -0.13628, 0.02839,
+ 0.06591, -0.03279, 0.26782, 0.35997, 0.55706,
+ -0.19844, -0.24698, 0.12995, 0.47276, 0.16038,
+ 0.42196, 0.15198, 0.03683, -0.30266, -0.11143,
+ -0.05902, -0.38219, -0.39130, -0.39425, -0.13515,
+ -0.04240, 0.03792, 0.06369, -0.01985, 0.21583,
+ 0.46233, -0.01354, 0.00686, -0.24132, -0.14651,
+ 0.12174, 0.69167, 0.20239, -0.27365, 0.24653,
+ -0.28357, -0.47219, -0.18511, 0.05113, -0.26224,
+ -0.09083, -0.04460, 0.10677, -0.11069, 0.10144,
+ -0.08763, 0.35046, 0.00992, -0.03189, 0.42508,
+ -0.06701, 0.45522, 0.44558, 0.10689, 0.06688,
+ -0.02707, -0.39859, -0.15157, 0.10697, 0.30113,
+ -0.34374, -0.33638, -0.39658, 0.40733, 0.32615,
+ 0.00429, 0.06340, 0.26357, -0.07578, -0.75623,
+ 0.03233, 0.35865, 0.19986, 0.58200, -0.34198,
+ -0.02461, 0.07744, 0.34965, -0.11413, -0.38783,
+ -0.00618, -0.43175, 0.08340, 0.37477, 0.13981,
+ 0.09984, 0.45192, 0.22841, 0.05812, -0.24822,
+ -0.02721, -0.19068, -0.13280, 0.07499, -0.10044,
+ 0.06061, 0.22100, -0.24973, -0.00460, -0.15375,
+ -0.16305, 0.36711, -0.37754, -0.07342, 0.09207,
+ -0.41675, -0.03503, 0.22543, 0.41697, 0.52551,
+ -0.32886, 0.02467, 0.18356, 0.10876, 0.21926,
+ 0.28689, 0.00677, -0.23805, 0.09456, -0.12467,
+ -0.13432, -0.11876, 0.02190, -0.30144, -0.24181,
+ -0.34628, 0.10451, 0.06555, 0.30236, 0.28325,
+ 0.69580, -0.17523, -0.13498, -0.00314, -0.01299,
+ 0.14536, 0.48372, 0.03599, -0.03181, 0.19609,
+ 0.18497, -0.19993, -0.39320, 0.01793, 0.02650,
+ 0.52980, -0.39752, 0.15516, -0.06609, -0.12542,
+ 0.08939, -0.05245, -0.15066, 0.07051, 0.17842,
+ 0.28194, 0.23054, 0.13960, 0.06117, -0.28235,
+ 0.02108, -0.33528, -0.16415, -0.18550, -0.28487,
+ 0.02460, 0.24638, 0.34547, -0.12340, 0.03855,
+ 0.25858, 0.32393, 0.09918, -0.22299, 0.04365,
+ 0.05840, 0.30245, -0.01840, 0.00072, 0.14709,
+ 0.21233, 0.27421, 0.35243, -0.19978, 0.14528,
+ 0.08666, -0.23715, -0.01929, -0.21062, 0.16652,
+ -0.17677, 0.01438, 0.26836, -0.26153, -0.03662,
+ -0.17614, -0.05878, 0.08105, 0.23845, 0.03144,
+ 0.19793, 0.07262, -0.14039, -0.14005, 0.20876,
+ 0.04277, 0.29848, 0.08132, -0.31135, -0.14070,
+ 0.28448, -0.17107, 0.22203, 0.24847, 0.06615,
+ -0.35032, -0.12580, -0.07233, -0.03343, -0.45603,
+ 0.01476, -0.19975, -0.07334, -0.14479, -0.19283,
+ 0.05788, 0.09449, 0.08351, -0.18010, 0.17206,
+ -0.26714, 0.12880, -0.34508, -0.13768, 0.34003,
+ 0.32165, -0.06869, 0.27104, 0.30170, -0.34377,
+ 0.17611, -0.03876, -0.05714, -0.10354, -0.01415,
+ -0.01382, 0.05265, 0.18568, -0.09858, 0.05681,
+ 0.08543, -0.51749, 0.45879, -0.07994, -0.23838,
+ 0.03481, 0.37689, -0.03496, -0.03259, 0.02850,
+ -0.22837, -0.16110, -0.12268, 0.05097, -0.00125,
+ -0.32863, 0.48587, -0.09395, 0.05322, 0.30065,
+ -0.34185, -0.51913, -0.27165, -0.20889, -0.03849,
+ 0.08574, 0.30619, 0.06371, -0.20344, 0.21360,
+ 0.12875, -0.14118, -0.00283, -0.10355, -0.12147,
+ -0.17311, -0.30375, 0.00889, -0.43512, 0.02158,
+ 0.19971, 0.04086, -0.24041, -0.04392, -0.26577,
+ -0.18659, -0.00896, 0.19065, -0.17351, -0.07984,
+ 0.51022, 0.11865, -0.02982, -0.18560, 0.38998,
+ -0.27873, 0.20779, -0.02954, 0.08870, -0.11180,
+ -0.37805, -0.02331, -0.15063, -0.38763, 0.08176,
+ -0.11063, -0.07194, 0.10890, 0.18629, 0.29787,
+ -0.29862, -0.07059, 0.64829, -0.02738, -0.32454,
+ 0.32090, -0.30040, -0.26210, 0.29378, 0.30565,
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+ -0.12229, -0.16909, -0.18625, 0.22424, 0.08049,
+ 0.60672, 0.25901, -0.20063, 0.24639, -0.30431,
+ 0.56112, 0.18389, -0.07497, 0.41305, -0.18735,
+ -0.27046, 0.29482, 0.24521, 0.40614, -0.10608,
+ 0.08220, -0.41945, -0.30048, -1.42807, 0.10022,
+ 0.14139, -0.10692, -0.46050, -0.11285, 0.06882,
+ 0.09809, 0.28004, 0.01042, 0.57719, 0.64496,
+ 0.16892, -0.41815, 0.00162, 0.40064, 0.09567,
+ -0.06512, 0.55018, 0.07722, -0.27798, -1.04702,
+ 0.09925, 0.30591, 0.13862, 0.10836, -0.26571,
+ 0.22523, 0.20883, 0.31875, 0.26194, 0.19042,
+ -0.03234, 0.42668, -0.27011, 0.32538, 0.58383,
+ -0.34137, -0.46360, -0.36319, 0.12852, -0.36559,
+ -0.84177, 0.60362, 0.54766, -0.31145, 0.34374,
+ -0.63696, -0.24864, 0.24972, 0.33502, 0.07228,
+ 0.21366, 0.33195, -0.56544, -0.65529, 0.44168,
+ 0.50887, 0.02173, -0.59473, -0.11482, 0.29673,
+ -0.04282, -0.74992, -0.01723, 0.15025, 0.02535,
+ 0.44557, -0.42716, 0.00725, 0.09973, -0.08813,
+ 0.19058, -0.04283, 0.08476, 0.53228, -0.24726,
+ 0.27707, 0.53229, 0.14837, -0.42043, 0.65416,
+ -0.24508, -0.16035, -0.66359, 0.12626, 0.33602,
+ 0.21686, 0.00917, -0.31169, -0.11892, 0.01757,
+ 0.30961, 0.15081, -0.09577, -0.48051, 0.28180,
+ -0.22171, 0.01448, 0.13450, 0.29634, -0.33526,
+ 0.38809, -0.16370, 0.01493, -0.73232, 0.49232,
+ 0.53611, 0.07025, -0.49107, 0.16772, 0.09125,
+ 0.52625, 0.71144, -0.16609, 0.05582, -0.44534,
+ 0.12767, -0.12572, 0.17578, -0.30485, 0.24000,
+ -0.48377, 0.41443, -0.00616, -0.24582, -0.52983,
+ 0.42687, 0.74135, -0.14477, -0.42101, -0.21596,
+ 0.26258, 0.06985, 0.75734, -0.27263, 0.15775,
+ 0.13600, 0.23888, -0.63301, 0.05320, 0.27954,
+ -0.07999, -0.30040, -0.07902, -0.31715, -0.43286,
+ -0.45979, 0.03641, 0.02982, 0.27578, -0.08083,
+ 0.27812, 0.40023, 0.14788, 0.11790, -0.33196,
+ -0.13339, -0.21537, 0.53587, -0.00332, 0.10341,
+ 0.08101, 0.16658, -0.54345, 0.01375, -0.18902,
+ 0.04198, -0.32772, 0.10853, 0.30759, -0.34146,
+ 0.18773, 0.03335, -0.11816, -0.53545, 0.75481,
+ 0.07576, -0.13262, 0.42122, -0.16957, -0.10810,
+ 0.47010, -0.43812, 0.28337, -0.30307, 0.21163,
+ -0.04907, -0.17678, -0.29085, -0.43068, -0.39284,
+ -0.71320, 0.61619, -0.18292, 0.06293, 0.14204,
+ 0.30417, 0.07351, 0.27912, -0.21847, 0.13913,
+ 0.43380, 0.05938, -0.31812, 0.41050, -0.00432,
+ 0.16404, -0.40716, -0.12905, -0.25542, -0.36725,
+ 0.31487, -0.12502, 0.36870, 0.10252, 0.04387,
+ 0.27838, 0.48376, -0.04287, 0.22137, 0.45062,
+ 0.78318, -0.21322, -0.21140, 0.09056, 0.12244,
+ 0.08313, -0.58632, -0.09702, -0.30302, -0.33142,
+ -0.32111, 0.41636, 0.00218, -0.32214, -0.02911,
+ -0.03803, 0.01158, 0.14407, 0.07617, 0.24474,
+ 0.02331, 0.66189, -0.29784, -0.31026, 0.82603,
+ -0.09831, 0.01894, 0.03884, -0.23090, -0.25700,
+ -0.11336, -0.09624, -0.37023, -0.01690, -0.17627,
+ 0.11532, 0.16059, -0.36181, 0.46701, 0.41919,
+ 0.41983, 0.11771, 0.14136, -0.01189, -0.07629,
+ 0.06738, 0.40874, -0.12724, -0.43350, 0.44081,
+ -0.22231, -0.37046, 0.09855, 0.13639, -0.14410,
+ -0.51902, 0.12433, 0.27680, 0.04359, 0.06145,
+ 0.14812, -0.24445, -0.16464, 0.39894, -0.17017,
+ 0.09276, 0.20392, 0.10158, -0.47882, -0.14943,
+ 0.25118, 0.15850, -0.17376, -0.06299, 0.31107,
+ 0.02223, -0.16870, 0.50466, -0.00316, -0.14083,
+ 0.12705, 0.20515, 0.32834, -0.37332, 0.22344,
+ -0.29886, -0.02961, 0.24517, -0.01158, -0.11182,
+ -0.06291, -0.27783, 0.10899, -0.23617, -0.00170,
+ 0.03465, 0.08894, 0.07328, 0.13108, 0.41180,
+ 0.66065, -0.20906, 0.11050, -0.29398, 0.10010,
+ -0.15700, -0.76060, -0.41844, -0.02844, 0.29760,
+ 0.04192, -0.39176, 0.35114, -0.15589, -0.26362,
+ 0.14193, 0.55211, -0.35186, -0.08625, -0.14450,
+ 0.43444, 0.15772, -0.03441, 0.24859, -0.08442,
+ -0.33971, -0.40901, -0.56509, 0.16658, -0.37843,
+ -0.06476, 0.20982, -0.18380, 0.44975, -0.46755,
+ -0.04130, 0.35242, 0.17766, -0.07784, 0.04003,
+ 0.16518, 0.30147, 0.59840, -0.12764, -0.01449,
+ -0.12919, -0.30296, 0.17423, -0.22962, 0.29029,
+ -0.19535, -0.20182, 0.03669, -0.39555, -0.16776,
+ -0.24337, -0.31495, -0.06049, 0.22262, 0.01799,
+ 0.26730, 0.12637, 0.56500, -0.23212, -0.16995,
+ 0.04591, -0.19344, 0.50416, 0.40071, -0.32463,
+ 0.03140, 0.25785, -0.74387, -0.27889, 0.24131,
+ 0.08881, -0.47419, -0.13367, 0.11292, -0.03019,
+ -0.00179, -0.34509, 0.19221, 0.33774, 0.05327,
+ -0.16043, 0.17252, 0.42285, 0.36869, -0.02031,
+ -0.59631, 0.08022, 0.56147, -0.75432, 0.07544,
+ -0.18719, 0.30695, -0.33805, 0.10000, 0.43349,
+ 0.04456, -0.20302, -0.28564, 0.45565, -0.10717,
+ 0.45016, 0.23326, 0.38325, 0.32223, 0.21665,
+ -0.19817, -0.73176, -0.96820, 0.50682, -0.18200,
+ -0.34896, 0.19378, 0.07389, -0.58412, -0.09277,
+ 0.24857, -0.37356, -0.18932, 0.38158, 0.82874,
+ 0.06616, 0.39016, 0.47469, 0.46194, -0.74807,
+ -0.23522, 0.25694, -0.24023, -0.61771, 0.60610,
+ -0.38924, -0.02306, -0.24023, 0.26451, -0.36748,
+ -0.24267, 0.61447, -0.00678, 0.13897, 0.63208,
+ 0.30172, 0.30207, 0.50937, 0.06238, 0.47184,
+ -0.60598, -0.27695, 0.45019, -0.54525, -0.59886,
+ 0.40782, -0.11143, 0.16348, -0.18690, 0.18334,
+ -0.22765, -0.56485, -0.10508, -0.72620, 0.12898,
+ 0.15835, 0.60254, 0.48654, 0.23090, 0.10825,
+ -0.02961, -0.05181, -0.00321, -0.40436, -0.69782,
+ -0.26625, 0.42197, 0.56861, -0.21110, 0.07212,
+ 0.22237, -0.26980, -0.17933, 0.15487, 0.27411,
+ -0.93787, 0.19157, 0.25583, 0.46882, 0.27213,
+ -0.05735, -0.02089, -0.30955, 0.19109, 0.29931,
+ 0.03381, -0.43295, 0.39820, 0.35794, 0.02963,
+ 0.18890, 0.57866, -0.22172, -0.23133, -0.04589,
+ 0.10541, -0.45483, -0.00290, 0.47793, 0.02480,
+ -0.15672, -0.46488, -0.04659, -0.14024, -0.21318,
+ 0.54094, -0.04467, 0.10199, 0.01821, -0.19425,
+ 0.00758, 0.02701, 0.26977, 0.29672, -0.27337,
+ -0.04023, -0.43918, -0.38062, 0.11406, 0.33990,
+ -0.23395, 0.57337, 0.41022, 0.18505, -0.80909,
+ 0.14802, 0.47726, -0.31302, -0.46314, -0.09437,
+ 0.14100, 0.38395, 0.08118, 0.64169, -0.45837,
+ -0.06104, 0.44681, -0.53369, -0.49697, 0.25039,
+ 0.28338, 0.13131, -0.18260, 0.35714, 0.18091,
+ -0.22554, 0.28258, 0.45816, -0.14228, -0.21730,
+ 0.35319, -0.12298, -0.03484, -0.12369, 0.51912,
+ -0.09979, -0.19194, 0.23888, -0.26739, -0.73341,
+ 0.16238, 0.22311, 0.04896, -0.35523, -0.02126,
+ -0.03027, -0.40642, 0.59023, -0.34926, 0.11519,
+ 0.10861, 0.15752, -0.48995, -0.14484, 0.02848,
+ 0.85711, -0.22574, 0.10808, 0.18943, -0.07258,
+ 0.53801, -0.05358, 0.45863, 0.05736, -0.05522,
+ 0.47830, -0.44976, 0.07265, 0.51931, -0.22156,
+ -0.33032, 0.16303, 0.57502, -0.32837, -0.38561,
+ -0.56744, -0.00644, 0.09261, -0.22272, -0.09369,
+ -0.44032, -0.10679, -0.21073, 0.55352, 0.73148,
+ 0.20523, 0.29299, 0.24226, 0.18233, 0.04404,
+ 0.46556, -0.44809, -0.48057, 0.07548, -0.31082,
+ 0.07161, -0.57024, -0.22119, -0.22815, 0.46623,
+ -0.19154, 0.40885, -0.07057, 0.01412, 0.48333,
+ 0.53684, -0.26096, 0.21742, 0.24513, 0.07217,
+ -0.05011, 0.07590, -0.79039, -0.27787, 0.03377,
+ 0.25617, 0.47978, -0.43740, -0.57820, -0.43930,
+ -0.26307, 0.15986, 0.16460, 0.25330, -0.29276,
+ 0.57489, -0.43497, -0.42070, -0.00357, 0.01808,
+ -0.39812, 0.61094, 0.73536, -0.34335, -0.11637,
+ -0.03951, -0.00529, -0.37196, -0.19023, 0.52892,
+ -0.33733, -0.60222, -0.38329, 0.70024, 0.25793,
+ 0.13343, -0.12165, -0.33650, 0.02285, 0.04614,
+ 0.52708, -0.05007, 0.07796, 0.07165, 0.13319,
+ -0.00511, -0.17781, -0.37626, 0.05473, -0.16630,
+ -0.08668, -0.50022, 0.06995, 0.17316, 0.52088,
+ -0.40959, 0.50658, 0.38414, -0.43142, 0.15092,
+ 0.18935, 0.08973, 0.04121, 0.41398, 0.03060,
+ 0.46855, -0.58412, -0.19872, -0.58451, -0.14248,
+ -0.23528, -0.19840, 0.22761, 0.04715, -0.01873,
+ -0.13938, -0.17557, -0.35559, 0.49556, -0.14794,
+ 0.32876, 0.62165, -0.33358, -0.15837, 0.25820,
+ 0.14079, -0.00861, -0.14572, -0.27443, -0.05564,
+ 0.42294, 0.13686, 0.26943, -0.58412, 0.21274,
+ 0.18811, 0.02375, -0.32340, -0.00208, 0.65248,
+ -0.53697, 0.09160, 0.28292, -0.07308, -0.01808,
+ 0.05999, 0.25528, -0.96611, -0.15885, -0.05789,
+ 0.06688, 0.30830, 0.17288, -0.06374, -0.25957,
+ 0.22614, 0.05561, 0.09376, -0.66724, -0.10554,
+ 0.01652, -0.65419, 0.18977, 0.42631, -0.28252,
+ -0.43529, 0.23329, -0.03888, -0.21885, 0.22474,
+ 0.21990, -0.39932, -0.02379, 0.33617, 0.22841,
+ 0.78105, 0.25901, 0.41752, -0.09047, -0.13189,
+ 0.20852, 0.22273, -0.74536, 0.46137, 0.52718,
+ 0.21208, -0.42033, 0.09373, 0.34320, -0.39931,
+ 0.13084, 0.09126, -0.30494, -0.18899, 0.21627,
+ -0.31930, -0.05101, 0.43313, 0.02622, -0.33690,
+ -0.33492, 0.30301, 0.32168, -0.23211, 0.44285,
+ 0.47427, 0.69310, 0.50401, 0.59334, 0.03853,
+ -0.31183, -0.07571, -0.62718, -0.22601, -0.20964,
+ 0.24810, 0.35861, -0.77217, -0.38871, 0.35061,
+ 2.49847, -4.18213, 2.13060, -0.30781, -4.15071,
+ -1.35903, -2.50270, 4.18010, -2.13498, 0.30394,
+ 4.14777, 1.36790,
+};
+
+float const b41_3[(na*41+1)*5+(5+1)*2] = {
+ -0.30811, -0.00829, 0.01856, 0.01902, 0.28502,
+ 0.04874, 0.38222, -0.21206, -0.33484, -0.19737,
+ -0.26996, 0.27350, 0.02546, -0.10850, 0.00858,
+ 0.06889, 0.13534, -0.04214, -0.20601, 0.19451,
+ 0.09897, 0.01123, 0.30393, -0.14278, -0.08332,
+ -0.03012, 0.15552, 0.16009, -0.16400, -0.22141,
+ 0.16369, -0.29980, -0.23438, 0.27158, -0.11458,
+ -0.06565, -0.07368, 0.28014, -0.04522, -0.09672,
+ 0.15175, 0.14516, 0.10675, 0.06458, -0.29414,
+ 0.25056, 0.01909, -0.47313, -0.20683, 0.06633,
+ 0.46171, 0.06892, -0.01982, -0.09084, 0.03886,
+ -0.15717, -0.40994, 0.31408, 0.22629, 0.42076,
+ -0.18059, 0.21560, -0.19340, -0.12634, -0.13847,
+ 0.03511, 0.06635, 0.12269, 0.19185, -0.06492,
+ -0.07946, 0.03553, -0.08000, 0.03351, 0.22749,
+ 0.35461, 0.09966, -0.04568, -0.13781, 0.33607,
+ -0.02173, -0.38853, 0.01238, -0.22859, 0.22422,
+ -0.06378, -0.25318, -0.21351, 0.35810, 0.00554,
+ -0.15394, 0.08417, 0.02943, -0.04434, -0.57794,
+ 0.16815, 0.24549, 0.14806, 0.21740, 0.01541,
+ 0.17543, -0.28887, -0.03218, 0.16613, -0.01453,
+ 0.14759, 0.00944, 0.12003, 0.06028, -0.13599,
+ -0.17820, 0.14381, 0.00579, 0.16228, -0.19067,
+ -0.11902, 0.08841, -0.16812, 0.11504, -0.29903,
+ -0.13889, 0.10194, -0.06608, -0.19563, 0.40674,
+ 0.17389, 0.12272, 0.00226, -0.00228, -0.11633,
+ -0.10071, 0.37258, -0.20069, -0.16115, -0.08658,
+ -0.31817, -0.40638, -0.17670, 0.19430, 0.37859,
+ 0.11843, 0.11201, 0.27102, -0.29233, -0.29162,
+ 0.24080, 0.14103, 0.07190, -0.17131, -0.21104,
+ 0.13084, -0.02739, 0.23283, 0.01405, -0.31648,
+ 0.05143, -0.25002, -0.31868, -0.25941, 0.34889,
+ -0.09436, -0.32831, -0.11962, 0.45968, 0.02568,
+ 0.14789, 0.32119, 0.08962, -0.17839, 0.02416,
+ 0.36600, -0.08098, -0.22294, 0.01178, 0.04486,
+ 0.01094, 0.24175, -0.11998, -0.17924, 0.08095,
+ -0.23306, -0.08928, -0.21409, 0.01640, -0.15892,
+ -0.07126, 0.02803, -0.03067, 0.23314, 0.11911,
+ 0.03657, 0.41605, -0.21351, -0.33983, -0.10230,
+ 0.12701, -0.40903, 0.16260, -0.04731, -0.61613,
+ -0.03698, 0.15087, -0.14303, -0.09575, 0.30629,
+ 0.50889, 0.30589, -0.31901, -0.16316, -0.03967,
+ -0.01773, -0.04116, 0.09540, -0.13411, -0.01627,
+ 0.05860, -0.19053, -0.34682, -0.01765, -0.15358,
+ -0.07537, 0.25024, 0.29988, 0.10349, -0.01413,
+ 0.20634, 0.22552, -0.04653, 0.01172, 0.05930,
+ 0.14393, 0.07224, -0.09169, -0.01307, -0.18628,
+ -0.09298, 0.20481, 0.20435, -0.12996, 0.13814,
+ -0.12609, -0.17113, -0.47556, 0.17197, 0.07533,
+ -0.06627, -0.05162, 0.58997, 0.30780, 0.21276,
+ -0.15588, -0.00206, 0.15457, -0.12384, 0.23241,
+ 0.31184, -0.04759, -0.03432, -0.05139, -0.40671,
+ -0.15357, -0.09128, 0.11889, -0.22842, 0.20039,
+ 0.29872, -0.19465, -0.00443, 0.03818, -0.03989,
+ 0.07931, 0.32816, -0.15332, -0.30110, 0.05828,
+ 0.36421, 0.22951, 0.37057, -0.24741, -0.01199,
+ -0.22010, 0.00595, 0.19187, 0.08224, -0.13493,
+ 0.21971, 0.08144, -0.00404, 0.01235, -0.24440,
+ -0.03169, -0.18286, 0.12821, 0.00957, -0.04179,
+ -0.30447, 0.23592, 0.02656, -0.01036, -0.42573,
+ -0.02448, -0.13066, -0.34241, 0.05718, 0.04404,
+ 0.03830, 0.27896, -0.14275, -0.09178, 0.41816,
+ -0.11450, -0.17730, 0.06830, 0.29550, 0.32938,
+ -0.03507, 0.28204, 0.33609, -0.09336, -0.21330,
+ -0.40191, -0.03137, -0.13340, -0.25982, -0.10479,
+ 0.15588, -0.01009, -0.16559, -0.33785, -0.04994,
+ -0.05114, 0.30368, 0.19668, 0.20009, 0.19437,
+ 0.32176, -0.20009, -0.09393, 0.12922, 0.06298,
+ -0.06504, -0.14492, -0.18545, 0.00789, 0.03219,
+ -0.26921, 0.08446, -0.18589, 0.29948, -0.07323,
+ 0.22295, -0.00437, -0.01115, -0.02543, -0.04177,
+ 0.37163, 0.42296, -0.31141, 0.09374, -0.11661,
+ 0.13292, -0.05135, -0.05788, -0.36067, 0.08906,
+ -0.16279, -0.23655, -0.09554, -0.21008, 0.31940,
+ 0.17090, 0.27337, 0.23082, -0.35026, 0.11193,
+ 0.16911, 0.40551, 0.36196, -0.05234, 0.03437,
+ 0.07259, -0.09722, -0.24329, 0.13769, -0.46907,
+ 0.05740, -0.25792, -0.19613, 0.36041, -0.25958,
+ 0.30425, -0.34210, 0.17540, -0.10786, 0.02537,
+ 0.23741, 0.45324, 0.05975, 0.50582, -0.01511,
+ -0.17232, -0.01297, 0.08313, 0.09663, -0.28890,
+ -0.21693, 0.03491, -0.11449, 0.27460, -0.04041,
+ -0.03223, 0.03915, -0.16038, -0.10565, -0.00277,
+ 0.13971, 0.11169, -0.10891, 0.29853, 0.26155,
+ -0.23787, -0.28017, -0.31541, 0.24665, -0.01364,
+ 0.21106, -0.00431, -0.07215, -0.53795, -0.15757,
+ 0.16587, -0.19365, 0.30804, -0.19859, -0.48227,
+ -0.12232, 0.26586, -0.01900, 0.32519, 0.55032,
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+ 0.10464, 0.09923, -0.12186, 0.09478, -0.10086,
+ 0.10562, 0.07911, 0.09734, -0.09897, 0.08517,
+ 0.05808, 0.10639, 0.09973, -0.10504, 0.09797,
+ -0.10120, 0.09519, 0.09613, -0.10053, 0.10661,
+ -0.10528, -0.09660, 0.09459, -0.10393, -0.11977,
+ -0.09375, -0.10708, -0.11848, 0.09192, -0.10733,
+ 0.08736, 0.05859, -0.11050, -0.09932, -0.10610,
+ 0.10225, -0.10066, -0.12304, -0.10160, 0.09532,
+ -0.10679, 0.08665, -0.10590, -0.09936, -0.10002,
+ -0.10439, 0.09869, -0.08579, -0.11266, 0.09977,
+ -0.09755, -0.10727, 0.05783, -0.10827, 0.08043,
+ 0.09660, -0.10114, -0.09855, -0.10627, 0.09685,
+ -0.10455, 0.09836, -0.10132, 0.13274, 0.09683,
+ 0.08217, -0.10334, -0.09585, 0.09646, 0.08985,
+ -0.10505, -0.09761, 0.07404, -0.14387, -0.10069,
+ 0.09012, -0.11798, -0.10120, -0.10569, -0.11276,
+ -0.10032, 0.10054, -0.08993, -0.10115, -0.09451,
+ -0.08883, -0.11898, 0.09272, 0.10473, 0.10172,
+ 0.09472, -0.11375, 0.10310, -0.11924, -0.14800,
+ -0.09828, -0.11468, 0.07184, 0.09912, -0.09583,
+ 0.08755, -0.10058, 0.09664, -0.09610, -0.11367,
+ -0.08550, -0.09993, 0.07918, -0.09598, 0.09978,
+ 0.10257, 0.08543, 0.10727, 0.10565, 0.09355,
+ -0.15017, -0.10072, 0.09430, 0.09720, 0.09740,
+ -0.09781, -0.10661, -0.10184, 0.10405, 0.10348,
+ 0.09048, -0.09321, -0.09552, 0.07344, 0.09549,
+ -0.09400, -0.10529, 0.09337, 0.09641, 0.10134,
+ -0.12340, -0.15046, -0.10295, -0.09961, -0.10701,
+ 0.10162, 0.10052, 0.09999, 0.09715, -0.10228,
+ -0.09193, 0.10184, 0.08971, -0.09404, -0.12605,
+ 0.08398, 0.11166, 0.09157, -0.11438, 0.09534,
+ -0.10058, 0.09616, 0.04621, -0.10195, -0.09460,
+ 0.09593, 0.09918, -0.10228, 0.11275, 0.09709,
+ 0.09819, -0.09453, 0.09497, -0.10517, 0.09385,
+ 0.08727, 0.08563, 0.09036, -0.10364, -0.11239,
+ 0.10418, 0.09161, -0.10252, -0.15479, -0.09567,
+ 0.11652, 0.10340, 0.11120, 0.10227, -0.11429,
+ 0.09669, 0.10016, 0.09675, 0.08827, 0.09849,
+ -0.10213, 0.08150, 0.09408, -0.10639, -0.10956,
+ -0.10544, -0.10389, -0.09717, 0.08285, 0.03996,
+ 0.08407, -0.09368, 0.07689, -0.09766, -0.10141,
+ -0.10291, -0.09814, -0.10152, -0.09076, 0.09122,
+ -0.08648, -0.10030, -0.10906, 0.09634, -0.09768,
+ -0.10805, 0.10780, 0.09639, -0.10171, -0.12070,
+ 0.03602, 0.09439, 0.09660, -0.11644, 0.10086,
+ -0.09956, -0.10700, 0.10860, 0.10243, -0.09864,
+ 0.09069, 0.11716, 0.09467, 0.09336, 0.09718,
+ -0.09969, 0.10328, -0.11318, 0.09443, 0.09992,
+ -0.11598, 0.03555, -0.09229, 0.10748, -0.12208,
+ 0.10154, -0.09445, 0.09347, 0.09723, 0.10109,
+ 0.09470, -0.10546, -0.09175, -0.09968, 0.09889,
+ 0.10159, 0.10185, -0.10828, -0.11431, 0.09212,
+ 0.09869, 0.08326, -0.16536, 0.09303, 0.08913,
+ 0.08721, -0.10025, -0.10210, -0.08658, 0.09846,
+ 0.09720, 0.10149, -0.09472, 0.08725, -0.09523,
+ -0.11482, -0.08396, 0.09570, -0.10881, -0.10969,
+ -0.09469, -0.10301, 0.08772, 0.03132, 0.09856,
+ 0.09043, 0.08383, -0.09337, -0.10340, 0.10902,
+ 0.10004, -0.10240, 0.09655, 0.09564, 0.10685,
+ -0.11049, -0.11523, 0.09612, 0.09907, 0.09666,
+ -0.10230, 0.09516, 0.11730, 0.08993, -0.17116,
+ 0.09957, -0.10453, 0.09294, -0.09819, -0.10497,
+ 0.07998, -0.10129, 0.10171, -0.10381, -0.10214,
+ -0.10787, 0.10372, 0.09122, -0.09476, -0.09446,
+ 0.09322, 0.09527, -0.10325, 0.11263, -0.09842,
+ -0.17819, -0.10573, -0.10795, -0.10663, 0.10206,
+ -0.09805, -0.11461, -0.09519, 0.10432, -0.10100,
+ 0.11841, -0.11435, -0.09176, -0.10123, 0.09477,
+ 0.09376, 0.09708, 0.09245, -0.09514, -0.10361,
+ -0.11038, -0.17860, -0.22272, 0.12524, -0.56268,
+ 0.26840, 0.23233, -0.44100, 0.37720, -0.62698,
+ 0.28496, 0.41280, -0.14630, 0.49940, 0.00467,
+ 0.30196, 0.27266, -0.03181, 0.74965, -0.09397,
+ -0.29492, 0.04800, -0.07114, -1.19046, 0.05794,
+ -0.29490, -0.24443, -0.09291, -0.12036, 0.02607,
+ 0.07501, 0.05890, -0.16576, 0.44965, 0.81009,
+ 0.26651, -0.10333, 0.30431, 0.27926, 0.06203,
+ -0.04195, 0.00041, 0.40129, -0.33179, -0.84734,
+ -0.22705, 0.27989, 0.24447, 0.08943, -0.19532,
+ 0.04812, 0.12586, -0.00640, 0.29023, 0.13187,
+ 0.33028, 0.47070, -0.20387, 0.16191, 0.77757,
+ -0.13152, -0.63613, -0.36244, 0.62924, -0.92468,
+ -0.59166, -0.09316, 0.58024, -0.36761, 0.19090,
+ -0.47114, -0.24049, 0.15679, 0.07379, -0.02342,
+ 0.42090, 0.71865, -0.25854, -0.39377, -0.15757,
+ 0.24617, 0.21921, -0.44338, 0.05916, 0.65686,
+ -0.24919, -0.70441, -0.15747, -0.04599, 0.05644,
+ 0.28520, -0.26881, 0.23467, 0.03485, 0.05431,
+ 0.15018, -0.08872, 0.36258, 0.09765, -0.33884,
+ 0.02459, 0.10726, 0.49923, -0.45059, 0.71427,
+ 0.27227, -0.17265, -0.63630, -0.30647, 0.12650,
+ 0.40191, 0.16680, -0.23426, -0.07656, 0.05057,
+ 0.24801, 0.02297, 0.18088, -0.62699, -0.00718,
+ -0.10707, -0.02815, 0.09417, 0.52716, -0.20718,
+ 0.47690, -0.17297, -0.16380, -0.72557, 0.29816,
+ 0.18994, 0.07205, -0.29128, 0.19899, -0.05669,
+ 0.23437, 0.26237, -0.04217, 0.18694, -0.00577,
+ 0.11683, -0.37521, 0.40667, -0.29439, 0.38577,
+ -0.40329, 0.22055, 0.45504, -0.21541, -0.63049,
+ -0.15392, 0.65827, -0.48288, -0.50619, 0.04419,
+ 0.17755, -0.00124, 0.92804, -0.50194, 0.63593,
+ 0.23695, 0.08251, -0.61622, -0.17690, 0.18380,
+ -0.14522, -0.18143, 0.06974, 0.15942, -0.35911,
+ -0.53785, -0.07487, -0.00527, -0.10865, 0.30857,
+ -0.01413, 0.40478, 0.11399, 0.27685, -0.17836,
+ -0.00228, 0.00687, 0.10806, -0.37031, -0.00996,
+ -0.02272, 0.27931, -0.17762, 0.02517, 0.03013,
+ 0.13175, -0.38365, 0.12290, 0.26261, -0.41166,
+ 0.41618, 0.07867, -0.04298, -0.22103, 0.74519,
+ -0.11393, -0.02769, 0.24766, -0.13373, -0.22864,
+ 0.36086, -0.28505, -0.02836, -0.32565, -0.13198,
+ 0.13271, -0.00374, -0.31409, -0.03239, -0.45799,
+ -0.27813, 0.26585, -0.04897, 0.33280, 0.06610,
+ 0.45664, 0.14108, 0.06846, 0.04160, 0.23193,
+ -0.00499, -0.12267, -0.23429, 0.22901, -0.35242,
+ 0.08393, -0.28010, -0.29585, -0.29651, -0.22452,
+ -0.01597, 0.29145, 0.22672, 0.18907, 0.16740,
+ -0.03717, 0.43988, -0.01398, 0.32118, 0.42253,
+ 0.87519, -0.28047, -0.29791, -0.12616, 0.02745,
+ -0.13158, -0.58516, -0.08648, 0.00010, -0.30171,
+ -0.13826, 0.59431, 0.12959, -0.54551, 0.06323,
+ -0.05931, -0.21591, 0.31929, -0.04654, 0.30084,
+ -0.10484, 0.64111, -0.32595, -0.48134, 0.47409,
+ -0.27390, -0.12674, 0.17677, 0.47464, -0.48637,
+ -0.10175, 0.17174, -0.37010, -0.23994, -0.14205,
+ -0.27625, 0.07304, -0.22197, 0.58097, 0.42549,
+ 0.40892, -0.16601, 0.08117, -0.06478, -0.54738,
+ 0.38454, 0.43746, 0.04074, -0.23479, 0.47227,
+ -0.09455, -0.37400, 0.00130, -0.10614, -0.00762,
+ -0.33528, -0.33870, 0.51792, 0.09755, 0.13472,
+ 0.19600, 0.27325, -0.24609, 0.25420, -0.44804,
+ -0.05443, 0.20853, -0.01508, -0.12471, -0.18857,
+ 0.29792, 0.00723, -0.20168, 0.04943, 0.32452,
+ 0.33625, -0.24470, 0.28102, -0.24502, -0.10197,
+ 0.48369, 0.29303, -0.07950, -0.08637, 0.28987,
+ -0.86425, -0.06835, 0.66244, -0.08230, 0.06826,
+ -0.10100, -0.31871, -0.16772, -0.36964, -0.28733,
+ 0.41463, -0.29101, 0.24875, 0.22321, 0.34153,
+ 0.63434, -0.14715, 0.21170, -0.13516, -0.22578,
+ -0.10509, -0.50732, -0.24247, -0.20354, 0.23815,
+ 0.20252, -0.39412, 0.19027, -0.34336, -0.37526,
+ -0.09823, 0.57685, -0.20961, -0.14665, 0.08665,
+ -0.02144, 0.33466, -0.23137, 0.20823, 0.12199,
+ -0.43352, -0.16896, -0.50472, 0.11180, -0.13341,
+ -0.00968, -0.08658, -0.21002, 0.17676, -0.17994,
+ -0.12396, 0.32361, 0.07183, -0.15817, 0.09530,
+ -0.13767, 0.18962, 0.51402, -0.05125, -0.01243,
+ -0.10787, -0.02465, 0.53378, -0.48743, 0.27017,
+ -0.14258, -0.51413, 0.38689, -0.19519, -0.21824,
+ -0.27603, -0.42296, 0.42215, 0.02306, 0.03842,
+ 0.22622, -0.10538, 0.62031, 0.06147, 0.06735,
+ 0.28475, -0.08795, 0.70965, 0.01750, -0.50644,
+ 0.10602, 0.35262, -1.09821, -0.48838, 0.16999,
+ -0.31008, -0.11443, -0.22234, 0.43173, 0.18474,
+ 0.06493, -0.33103, 0.17085, -0.13693, -0.00074,
+ -0.24995, 0.49488, 0.34220, 0.06650, -0.02127,
+ -0.67008, -0.32218, 0.62489, -0.54765, -0.06838,
+ -0.04475, 0.40469, -0.26465, 0.10000, 0.46036,
+ 0.05831, -0.29921, -0.25416, 0.18182, 0.17635,
+ 0.20313, -0.07662, 0.46913, 0.20189, 0.12107,
+ 0.32657, -0.99278, -0.77465, 0.41148, -0.37031,
+ -0.37250, 0.43346, 0.12411, -0.47365, -0.07127,
+ 0.20012, -0.21522, -0.30172, 0.34664, 0.77463,
+ 0.28740, 0.27654, 0.24269, 0.20951, -0.72815,
+ -0.06280, 0.06623, -0.21589, -0.22233, 0.79108,
+ -0.37101, -0.22849, 0.09633, 0.09285, -0.54943,
+ -0.27984, 0.15845, 0.02663, -0.17753, 0.54514,
+ 0.65879, 0.64883, 0.36953, -0.01562, 0.34233,
+ -0.74001, -0.20127, 0.46271, -0.29849, -0.52431,
+ 0.32603, -0.00964, 0.29947, -0.38467, 0.21304,
+ -0.18258, -0.49084, -0.20954, -0.23358, -0.01029,
+ 0.01342, 0.75621, 0.79617, 0.34765, -0.14900,
+ -0.03738, -0.09475, -0.21008, -0.40799, -0.25722,
+ -0.44988, 0.14380, 0.54048, -0.04242, -0.09742,
+ -0.21741, -0.06941, -0.13970, 0.27719, -0.51420,
+ -0.93518, 0.43274, 0.18856, 0.77905, 0.22224,
+ 0.03151, 0.33841, -0.16134, 0.46691, 0.13006,
+ -0.02205, -0.84080, 0.53223, -0.05583, 0.27517,
+ -0.05877, 0.61974, 0.08991, -0.30484, -0.23834,
+ -0.18297, -0.51211, 0.24964, 0.33129, 0.07219,
+ -0.00492, -0.37804, -0.05806, -0.46518, -0.13187,
+ 0.50713, -0.11570, -0.25133, 0.06506, -0.14508,
+ 0.23575, 0.14669, 0.26640, 0.57016, -0.22894,
+ -0.31754, 0.22848, -0.29824, 0.24946, 0.45848,
+ -0.34739, 0.51851, -0.02269, 0.42266, -0.60979,
+ 0.02888, 0.88949, -0.63616, -0.38732, 0.32240,
+ 0.17446, 0.00681, 0.18246, 0.37854, -0.74509,
+ -0.32540, 0.21918, -0.63254, -0.51585, 0.23369,
+ 0.35451, 0.05695, -0.06082, 0.09063, 0.14110,
+ -0.58916, 0.21005, 0.19263, -0.17250, -0.03855,
+ 0.69830, 0.09322, 0.18985, -0.13894, 0.54741,
+ 0.17707, -0.14800, 0.13634, -0.15155, -0.88862,
+ 0.18902, 0.27051, 0.30784, -0.11374, -0.04936,
+ 0.08863, -0.88326, 0.29969, -0.03976, -0.04544,
+ 0.13921, 0.24176, 0.00238, -0.53995, -0.07529,
+ 0.62692, -0.09013, 0.11013, -0.00596, 0.35734,
+ 0.23105, -0.00922, 0.45969, 0.62209, -0.20465,
+ -0.20113, -0.12746, 0.16803, 0.42613, 0.03993,
+ -0.28980, -0.20000, 0.41831, -0.46047, -0.42879,
+ -0.13657, -0.30873, 0.32787, -0.38125, -0.29992,
+ -0.00749, 0.37468, -0.28773, 0.31999, 0.82251,
+ 0.12414, 0.32643, 0.27477, 0.13598, 0.14344,
+ 0.45162, -0.16183, -0.59174, 0.28053, -0.23945,
+ -0.66793, -0.80929, -0.39314, -0.16527, 0.49995,
+ -0.65294, 0.50068, 0.03829, 0.14486, 0.36510,
+ 0.50879, -0.05019, 0.01024, -0.02732, -0.05007,
+ 0.27436, 0.14085, -0.55710, 0.00583, -0.05883,
+ -0.22732, 0.14420, -0.48182, -0.24978, -0.51005,
+ 0.08144, -0.01447, 0.16027, 0.11982, -0.13939,
+ 0.44871, -0.47802, -0.53620, -0.30372, -0.11380,
+ -0.20996, 0.55828, 0.49979, -0.22860, -0.01715,
+ 0.37197, -0.42371, -0.12812, 0.20133, 0.38758,
+ -0.41111, -0.36764, -0.23788, 0.58126, 0.12368,
+ 0.23447, -0.10145, -0.21256, -0.24735, 0.10957,
+ 0.30523, -0.07893, 0.22690, -0.36582, -0.49464,
+ 0.21247, 0.13214, -0.28870, 0.32556, -0.17564,
+ -0.48471, 0.10030, 0.04931, 0.03439, 0.55167,
+ -0.95263, 0.23781, 0.04875, -0.31087, 0.14685,
+ 0.32677, 0.23980, 0.16617, 0.53729, -0.13951,
+ 0.32199, -0.03437, 0.28639, -0.63956, -0.16892,
+ -0.33027, -0.29619, 0.19874, 0.09119, -0.27060,
+ 0.37946, -0.46153, -0.42953, 0.50891, 0.02222,
+ 0.53916, 0.53229, -0.16212, -0.50460, -0.08985,
+ 0.30100, 0.23940, -0.24430, -0.28054, -0.10376,
+ 0.18506, 0.19991, -0.27969, -0.01053, 0.30939,
+ 0.32167, 0.02754, -0.49761, 0.07784, 0.75918,
+ -0.14514, 0.00558, 0.38484, -0.12415, -0.25198,
+ -0.27626, 0.30685, -0.64863, 0.15844, -0.49409,
+ -0.02492, -0.22053, 0.09150, -0.11948, 0.15299,
+ 0.22184, 0.18321, 0.04949, -0.47523, 0.01489,
+ -0.11921, -0.31141, 0.23426, 0.46426, -0.30068,
+ -0.72816, 0.20881, 0.09817, 0.33321, 0.14036,
+ -0.24339, -0.32460, -0.16293, 0.33844, 0.01277,
+ 0.33147, 0.26215, 0.46087, -0.15430, -0.39994,
+ 0.62228, -0.00179, -0.23533, 0.26457, -0.01268,
+ 0.21692, -0.32824, 0.32218, 0.04176, 0.18459,
+ 0.32155, -0.52592, -0.29497, 0.10278, 0.31192,
+ -0.46744, -0.35353, 0.45449, 0.24549, 0.10581,
+ -0.52501, 0.27879, 0.16075, 0.01680, 0.48076,
+ 0.15056, 0.75463, 0.48547, -0.00064, 0.21361,
+ 0.03184, -0.05760, -0.54232, -0.35716, -0.14254,
+ -0.17570, 0.06215, -0.53062, -0.29002, 0.22778,
+ 2.10816, -3.81627, 2.26752, 0.12074, -4.16963,
+ -1.01620, -2.11111, 3.81530, -2.27023, -0.12238,
+ 4.16850, 1.02115,
+};
+
+float const b41_4[(na*41+1)*5+(5+1)*2] = {
+ -0.43773, -0.16176, -0.12301, 0.27999, 0.19277,
+ 0.04312, 0.27404, -0.21202, -0.23789, -0.25574,
+ -0.30260, 0.43932, 0.28096, -0.23779, 0.20923,
+ 0.10576, 0.23583, -0.00282, -0.25199, 0.03465,
+ 0.23119, 0.03241, 0.16354, 0.05268, -0.07005,
+ -0.02804, 0.22325, 0.17320, -0.10683, -0.30546,
+ 0.05554, -0.33557, -0.19389, 0.29915, 0.06780,
+ -0.03591, -0.10218, -0.03727, 0.12826, 0.08151,
+ -0.00482, 0.23107, 0.06718, 0.19932, -0.30110,
+ 0.13452, -0.03696, -0.37985, -0.20786, -0.06755,
+ 0.29831, 0.09279, 0.09607, 0.16083, 0.01393,
+ -0.20795, -0.31112, 0.28615, 0.20266, 0.51068,
+ -0.08134, -0.00432, -0.16301, -0.03075, -0.25908,
+ -0.15869, -0.04391, -0.13655, 0.08819, -0.02627,
+ -0.05580, -0.06770, -0.30557, 0.12873, 0.22433,
+ 0.51766, 0.14733, -0.12665, 0.18704, 0.51460,
+ 0.04601, -0.07336, -0.01758, -0.28783, 0.00108,
+ -0.06638, -0.21867, -0.24435, 0.27953, -0.00749,
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+ -0.00438, -0.37711, 0.05309, 0.71719, -0.25116,
+ -0.11383, -0.06665, 0.67087, -0.14520, -0.29792,
+ -0.39505, 0.12116, 0.21174, -0.13783, -0.57937,
+ -0.45721, 0.11939, -0.06451, 0.21633, 0.56332,
+ 0.23004, 0.34055, 0.04769, -0.33419, 0.49785,
+ 0.28991, 0.40930, -0.53447, -0.02055, -0.46109,
+ -0.01595, -0.80479, -0.01646, -0.01665, 0.53930,
+ -0.47487, 0.50729, 0.19107, 0.45945, 0.25275,
+ 0.39215, -0.01530, 0.02674, 0.00401, -0.39592,
+ 0.21168, 0.33020, -0.73953, 0.18137, -0.22318,
+ 0.03707, 0.33613, -0.63530, -0.37717, -0.48434,
+ -0.26213, 0.04735, 0.28747, 0.11681, -0.22562,
+ 0.45751, -0.38317, -0.41829, -0.31819, -0.44015,
+ -0.19238, 0.69557, 0.61594, -0.36149, 0.10122,
+ 0.24113, -0.34367, -0.36933, 0.52412, 0.47115,
+ -0.43361, -0.68169, -0.28112, 0.65343, 0.27925,
+ 0.40364, 0.32156, -0.11191, -0.27385, -0.09344,
+ 0.47772, 0.04146, 0.07098, -0.03025, 0.06846,
+ -0.04765, 0.15453, -0.75882, -0.22464, -0.14728,
+ -0.53025, -0.09354, -0.13947, 0.05586, 0.51957,
+ -0.56026, 0.28177, 0.24887, -0.23313, 0.12820,
+ 0.06767, 0.15699, 0.33118, -0.00987, 0.26473,
+ 0.28439, -0.26076, 0.50273, -0.86052, -0.37324,
+ -0.24376, -0.16295, 0.04685, 0.11915, -0.05816,
+ 0.14879, 0.35809, -0.29907, 0.51182, -0.01341,
+ 0.36302, 0.15469, -0.35039, -0.02005, 0.36669,
+ 0.26659, -0.08377, -0.12428, -0.23535, -0.45317,
+ 0.19857, 0.23677, -0.42621, -0.40010, 0.25825,
+ 0.27302, -0.10830, -0.00131, 0.27393, 0.43165,
+ -0.63656, -0.18218, 0.06739, -0.38490, -0.30828,
+ 0.48620, 0.19395, -0.66790, -0.11450, 0.00596,
+ -0.21743, 0.14096, -0.10069, 0.37753, -0.16777,
+ 0.02012, 0.29856, -0.00821, -0.46739, 0.36656,
+ -0.14996, -0.51263, 0.23256, 0.22591, -0.19782,
+ -0.60622, -0.10861, 0.12291, 0.32004, 0.04663,
+ -0.20790, -0.57598, -0.11960, 0.19844, 0.04669,
+ 0.44243, 0.42255, 0.24952, -0.10375, -0.24924,
+ 0.23018, -0.22609, -0.02346, 0.17343, 0.09897,
+ 0.26523, -0.11561, 0.30893, 0.20257, 0.12163,
+ 0.62493, -0.06578, -0.46646, -0.16092, 0.03598,
+ -0.30628, -0.43808, 0.46204, -0.16868, -0.02077,
+ -0.60002, 0.26273, 0.15660, -0.32448, 0.22188,
+ 0.33135, 0.71421, 0.04429, 0.26267, 0.06667,
+ -0.00976, -0.31009, -0.45510, -0.08991, 0.73291,
+ 0.12421, 0.67206, -0.93888, -0.26540, 0.25118,
+ 1.96241, -4.21412, 2.26473, -0.79283, -3.69526,
+ -0.94100, -1.96690, 4.21116, -2.26988, 0.78718,
+ 3.69354, 0.95091,
+};
+
+float const b41_5[(na*41+1)*5+(5+1)*2] = {
+ -0.18140, -0.15868, -0.12863, 0.26817, 0.19866,
+ -0.03437, 0.09317, -0.26726, -0.52981, -0.14748,
+ -0.13563, 0.44797, 0.25663, -0.18930, 0.23855,
+ -0.09681, 0.36110, -0.11117, 0.02376, 0.08680,
+ 0.07649, 0.06314, 0.20024, 0.10887, -0.00384,
+ 0.02988, -0.05201, -0.03594, -0.05866, -0.32322,
+ 0.31157, -0.08316, -0.26983, 0.26564, -0.00071,
+ -0.07768, -0.15413, 0.31321, 0.07845, 0.08996,
+ -0.09434, 0.03851, 0.24046, -0.07100, -0.33416,
+ 0.04497, 0.10029, -0.43814, -0.04784, 0.06149,
+ 0.13774, 0.05748, 0.13774, -0.09914, 0.08868,
+ -0.07786, -0.30545, 0.02341, 0.54687, 0.42612,
+ -0.02679, 0.26640, -0.30473, 0.02786, -0.27446,
+ -0.17720, -0.06798, 0.04651, 0.10331, -0.17100,
+ 0.14122, -0.08302, 0.04786, 0.09115, 0.13127,
+ 0.30117, 0.11622, 0.12608, 0.10112, 0.30410,
+ 0.15871, -0.26337, 0.20322, -0.44609, 0.13659,
+ -0.13239, -0.27787, -0.13247, 0.08858, 0.07000,
+ -0.04506, 0.20349, 0.08972, -0.05377, -0.34819,
+ -0.13971, 0.36869, 0.39738, 0.20981, -0.09910,
+ 0.35261, -0.34095, -0.12852, 0.37575, -0.16733,
+ -0.02422, -0.06739, 0.06346, 0.15151, -0.14792,
+ 0.08023, 0.13796, -0.05698, -0.12606, 0.01654,
+ 0.01091, 0.04249, -0.11555, 0.07012, -0.41254,
+ -0.11619, 0.19469, 0.02262, 0.05162, 0.42389,
+ 0.01876, -0.14467, 0.07657, 0.05566, 0.04994,
+ 0.12373, 0.16662, -0.21442, -0.19434, -0.31309,
+ -0.14478, -0.07627, -0.01538, 0.16016, 0.32205,
+ -0.06996, 0.09666, 0.48434, -0.33824, -0.19407,
+ 0.30583, -0.07658, -0.02961, 0.00128, -0.12062,
+ 0.20099, 0.21685, 0.31571, 0.17026, -0.20652,
+ -0.13466, -0.08201, -0.24518, -0.04190, 0.26795,
+ -0.25979, -0.41323, -0.32231, 0.23155, 0.24407,
+ 0.24114, 0.11374, -0.17499, 0.00867, -0.03155,
+ 0.25686, -0.06249, -0.10955, -0.03128, 0.29544,
+ 0.00295, 0.29491, 0.06523, -0.11707, 0.14067,
+ -0.28816, -0.16373, -0.40283, -0.05862, -0.10313,
+ -0.12912, 0.01486, 0.08741, -0.02859, 0.24681,
+ -0.22741, 0.29027, -0.08451, -0.16937, 0.19767,
+ 0.14859, -0.38470, 0.20274, -0.02657, -0.47106,
+ -0.00651, -0.05837, -0.09287, -0.25217, 0.05943,
+ 0.32225, 0.25674, -0.08424, 0.21774, -0.23412,
+ 0.11818, -0.06318, 0.23047, -0.17197, 0.10860,
+ 0.01358, -0.20900, -0.13284, 0.27342, -0.33684,
+ -0.11742, 0.16097, 0.40610, 0.10382, 0.11604,
+ 0.16487, 0.11902, -0.29036, 0.15103, -0.04755,
+ 0.03549, 0.21204, -0.25765, 0.23174, -0.14249,
+ 0.01730, 0.29677, 0.23124, 0.13171, 0.08165,
+ -0.17276, -0.20904, -0.38132, 0.23151, 0.08233,
+ -0.22418, -0.02303, 0.54631, -0.04876, 0.17432,
+ -0.04992, -0.07384, 0.29361, -0.26563, 0.14925,
+ 0.16351, 0.01513, 0.33213, -0.19906, -0.34032,
+ -0.25734, -0.05990, -0.05510, -0.05573, 0.30009,
+ 0.12676, -0.00190, -0.08359, -0.01230, -0.23503,
+ 0.23353, 0.59676, -0.19802, -0.24467, 0.00277,
+ 0.26258, 0.19461, 0.24581, 0.08511, -0.24552,
+ -0.00172, -0.16444, 0.27406, 0.18994, -0.18626,
+ 0.00916, 0.23192, -0.12408, 0.33578, -0.05925,
+ -0.00757, -0.18643, 0.12929, -0.13944, -0.16915,
+ -0.28586, -0.18560, -0.00479, -0.19601, 0.01070,
+ -0.08620, -0.08573, -0.40839, 0.36839, 0.15060,
+ 0.12102, 0.05514, 0.02599, 0.09838, 0.28535,
+ -0.14299, -0.08864, 0.34712, 0.16049, 0.25210,
+ 0.17223, 0.14170, 0.19019, -0.20156, -0.30016,
+ -0.26633, -0.13839, 0.05231, -0.26821, -0.21347,
+ 0.42642, 0.07520, 0.13085, -0.30520, 0.17153,
+ -0.17048, 0.45757, 0.26953, 0.33353, -0.22296,
+ -0.08436, -0.20106, -0.25746, -0.05126, 0.07021,
+ 0.18094, -0.24798, -0.15859, -0.00511, 0.08247,
+ -0.33630, 0.14832, -0.09840, 0.45366, 0.05193,
+ 0.24169, 0.16450, 0.42015, -0.06953, -0.08873,
+ 0.23447, 0.08410, -0.47428, -0.04009, -0.03945,
+ 0.06434, 0.22109, 0.00700, -0.47186, 0.04108,
+ -0.32395, -0.25397, 0.14563, -0.20902, 0.23290,
+ 0.26178, 0.31413, 0.10567, -0.05620, -0.07506,
+ 0.24213, 0.66057, 0.23082, -0.29695, 0.09737,
+ -0.13151, 0.09013, -0.04266, 0.22221, -0.47018,
+ 0.17156, -0.42012, -0.09547, 0.31824, -0.02003,
+ 0.09333, -0.18384, 0.17978, 0.01009, 0.09771,
+ 0.33636, 0.28489, -0.00206, 0.38714, -0.14875,
+ -0.00932, -0.29780, 0.11110, -0.02150, -0.26729,
+ -0.13401, 0.03451, -0.16451, 0.30536, -0.05154,
+ -0.30310, -0.07733, -0.00054, 0.27964, 0.01074,
+ 0.20294, 0.18706, 0.14261, 0.41278, 0.15021,
+ -0.23210, -0.13741, -0.40105, 0.18253, 0.06605,
+ -0.30892, -0.06798, -0.04773, -0.41378, -0.22062,
+ 0.14247, -0.09820, 0.19763, -0.00456, -0.16169,
+ 0.02238, 0.26259, -0.06414, 0.44802, 0.51172,
+ 0.10000, -0.01605, 0.01764, 0.23349, 0.03484,
+ -0.11966, 0.19979, -0.20136, 0.10941, -0.15308,
+ -0.05485, 0.20667, 0.00523, 0.21563, 0.74121,
+ -0.06791, -0.06904, -0.10829, 0.21275, -0.00781,
+ 0.11942, 0.12707, -0.02835, -0.40700, -0.11465,
+ -0.12480, -0.16000, 0.09454, -0.23068, 0.05087,
+ -0.19810, 0.02401, -0.26494, -0.17835, 0.11145,
+ 0.39967, 0.03946, -0.02183, -0.13387, -0.02705,
+ 0.13703, 0.46297, 0.31062, -0.12431, 0.21643,
+ -0.21500, -0.46175, -0.04516, 0.07519, -0.28261,
+ -0.03043, -0.26146, 0.08191, 0.01570, -0.09993,
+ -0.02195, 0.23158, 0.01024, 0.19995, 0.26706,
+ 0.09776, 0.30165, 0.36971, 0.25682, -0.02089,
+ 0.33458, -0.45117, 0.00602, 0.23817, 0.31196,
+ -0.31815, -0.13854, -0.60088, 0.31871, 0.41417,
+ 0.05893, -0.20705, 0.27652, -0.08651, -0.39704,
+ 0.02347, 0.39707, -0.07792, 0.18094, -0.20744,
+ 0.04830, 0.17372, 0.21305, 0.13400, -0.33001,
+ 0.20992, -0.45011, 0.21589, 0.16543, 0.17810,
+ -0.00539, 0.23298, 0.10108, -0.09241, -0.20002,
+ 0.11771, -0.10946, -0.16808, -0.04057, -0.24045,
+ 0.37104, 0.21855, 0.09066, 0.21489, -0.11356,
+ -0.19073, 0.36115, -0.44743, 0.05098, -0.02315,
+ 0.02616, -0.13219, 0.07586, 0.44157, 0.09023,
+ -0.16629, -0.04661, 0.32001, 0.17610, 0.13827,
+ 0.03632, -0.05212, -0.31776, -0.08609, -0.00369,
+ -0.02967, -0.05031, 0.05466, -0.11183, -0.01574,
+ -0.12782, 0.16578, 0.15413, -0.08652, 0.57548,
+ 0.32037, -0.14279, -0.07309, 0.03631, 0.02714,
+ 0.02310, 0.31511, -0.04425, -0.22108, -0.12003,
+ 0.06998, -0.12125, -0.24753, 0.02583, 0.06482,
+ 0.40114, -0.36274, 0.19206, -0.10442, -0.11890,
+ 0.09720, 0.07730, 0.13853, 0.08038, 0.40525,
+ 0.24380, 0.16410, 0.30861, 0.01790, -0.06153,
+ -0.07428, -0.05470, -0.20652, -0.04963, -0.25457,
+ 0.03457, 0.09994, 0.14761, -0.09953, -0.16008,
+ 0.07368, 0.62146, 0.00963, -0.21184, 0.15371,
+ 0.11955, 0.25929, 0.09847, -0.01888, 0.06263,
+ 0.00599, 0.12969, 0.52332, -0.16095, 0.14178,
+ 0.03377, 0.12232, 0.20453, -0.30595, -0.03231,
+ -0.06109, -0.12357, 0.26111, -0.07948, 0.02812,
+ -0.34912, -0.01321, -0.00610, 0.23226, 0.14026,
+ 0.12919, -0.06261, -0.08105, 0.07130, 0.14927,
+ 0.14927, 0.17675, 0.12386, -0.27215, -0.42181,
+ -0.02496, -0.16391, 0.01874, 0.20126, 0.21770,
+ -0.30040, 0.05284, -0.24931, 0.12704, -0.08900,
+ 0.15649, -0.22632, -0.14063, -0.02107, 0.05608,
+ -0.02931, 0.24612, -0.00643, -0.26831, 0.17517,
+ -0.00671, -0.09094, -0.09460, -0.20507, 0.24888,
+ 0.05204, 0.09817, 0.41040, 0.03149, -0.15080,
+ 0.30712, -0.15877, -0.18368, 0.00415, -0.14624,
+ -0.00627, -0.00570, 0.13290, -0.23544, 0.09004,
+ 0.19522, -0.64571, 0.51530, -0.03369, -0.20291,
+ 0.10977, 0.27751, -0.04778, 0.28232, -0.09015,
+ -0.02980, -0.38804, 0.06410, -0.00750, -0.11873,
+ -0.26123, 0.57035, 0.00601, -0.01031, -0.06705,
+ -0.21118, -0.38523, -0.30435, -0.11526, 0.29132,
+ 0.01983, 0.06444, 0.03625, -0.25687, 0.30580,
+ 0.00969, -0.11711, 0.02595, 0.23794, -0.28307,
+ -0.20910, 0.15004, 0.00564, -0.31107, 0.00678,
+ -0.00319, -0.04949, -0.19273, -0.11460, -0.16711,
+ -0.17341, 0.06303, 0.35710, -0.18996, -0.05451,
+ 0.56998, 0.03298, -0.12141, -0.22432, 0.27469,
+ -0.41430, -0.09229, 0.12432, 0.29280, 0.01565,
+ -0.18915, -0.08627, -0.21980, 0.00000, 0.12837,
+ 0.07809, -0.11254, 0.01996, 0.12295, 0.47384,
+ -0.28261, -0.14410, 0.18282, 0.04339, -0.41228,
+ 0.27084, -0.35816, -0.21364, 0.13796, 0.30854,
+ -0.10441, -0.35180, -0.08199, 0.04273, -0.36510,
+ -0.33574, -0.23994, 0.36336, 0.23101, 0.03596,
+ 0.52004, -0.28291, 0.02176, 0.51926, -0.22652,
+ 0.04849, 0.11777, -0.31067, 0.17586, 0.17211,
+ 0.37192, -0.02163, 0.03240, 0.12515, 0.22169,
+ -0.29157, -0.11471, -0.20662, -0.03499, 0.18113,
+ 0.37509, 0.06608, -0.00386, -0.03175, 0.15576,
+ -0.14465, 0.25533, -0.03921, -0.18892, -0.24305,
+ -0.28851, 0.17918, 0.15769, 0.17348, -0.24409,
+ -0.03152, 0.16670, 0.05846, 0.08216, 0.41754,
+ -0.16078, 0.13316, 0.26104, -0.26851, 0.07898,
+ -0.22715, 0.33898, 0.18542, 0.06707, -0.42103,
+ 0.17375, -0.29021, 0.20006, -0.31575, -0.34896,
+ 0.12353, 0.10198, -0.23600, -0.14022, 0.16751,
+ -0.01366, -0.09372, 0.48162, 0.18748, -0.06543,
+ -0.11848, 0.05742, 0.07284, 0.13011, -0.06706,
+ 0.04204, 0.37522, 0.12148, -0.29504, 0.28346,
+ 0.22264, -0.15284, 0.71187, -0.17147, 0.06140,
+ 0.31577, 0.12159, 0.42929, -0.27192, 0.23671,
+ -0.04658, 0.01131, -0.07147, -0.06891, 0.48202,
+ -0.10545, -0.13395, -0.60842, -0.19819, 0.09895,
+ 0.27219, -0.20977, -0.68458, 0.46526, 0.22401,
+ -0.15153, 0.22921, 0.33857, 0.11156, 0.24273,
+ -0.07888, 0.14010, -0.26049, 0.10294, -0.54468,
+ 0.20547, 0.25920, -0.14621, 0.00662, -0.11415,
+ 0.00251, 0.29832, -0.23014, -0.29423, 0.73165,
+ -0.06265, -0.31204, -0.21425, 0.33136, 0.10336,
+ 0.13191, -0.38080, -0.03943, -0.50970, 0.61910,
+ 0.40677, 0.45901, -0.29044, -0.02572, 0.16970,
+ 0.28664, -0.07209, 0.29652, 0.15429, -0.30773,
+ 0.48283, 0.65291, -0.43998, -0.46746, 0.03670,
+ 0.50733, 0.15428, -0.19279, -0.35848, 0.34175,
+ -0.05711, -0.19000, 0.28902, -0.16797, -0.11118,
+ 0.38558, 0.53299, 0.06196, 0.29627, 0.13113,
+ -0.09471, -0.13493, 0.38544, 0.07272, -0.03341,
+ -0.07940, -0.54619, 0.16079, -0.14079, 0.09822,
+ -0.05466, 0.08304, -0.20567, 0.24244, 0.08249,
+ -0.16454, 0.10506, 0.57443, -0.47617, 0.21151,
+ -0.34915, 0.18510, -0.26233, 0.26566, 0.44634,
+ 0.30408, 0.03484, -0.12528, 0.16200, -0.55822,
+ -0.18316, 0.44873, 0.35501, 0.05515, -0.00610,
+ 0.14668, -0.19444, -0.21079, 0.27325, -0.19407,
+ -0.17282, -0.43886, 0.42914, -0.14066, 0.05378,
+ 0.34960, 0.15129, 0.47469, 0.07323, 0.25778,
+ 0.19782, -0.50119, -0.18544, -0.28023, 0.09822,
+ 0.25715, -0.00455, 0.44675, -0.42785, 0.51061,
+ -0.30321, 0.01408, -0.52179, -0.44103, -0.02934,
+ 0.14176, 0.39581, 0.32952, 0.23568, -0.07646,
+ -0.05731, -0.16824, 0.06991, -0.17058, 0.48289,
+ 0.13029, 0.09072, 0.35323, -0.35861, -0.26876,
+ 0.05949, -0.21990, -0.44319, -0.30708, 0.36272,
+ -0.36271, -0.18001, 0.44994, 0.25602, 0.11169,
+ 0.22128, -0.22991, 0.27063, 0.05907, -0.31003,
+ -0.02975, 0.04148, 0.30907, 0.53912, 0.09676,
+ 0.16743, 0.12127, 0.05255, 0.15928, 0.01693,
+ 0.36124, -0.02472, -0.38783, 0.18964, -0.00731,
+ 0.47513, 0.08227, -0.53734, -0.15396, -0.26568,
+ 0.20752, -0.08836, 0.21160, 0.23672, 0.09205,
+ -0.30052, -0.07699, 0.08790, -0.49846, -0.46290,
+ 0.64909, 0.20116, 0.25287, 0.16771, 0.43418,
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+ -0.33922, 0.17953, 0.33041, -0.05544, 0.25868,
+ 0.08930, -0.25018, -0.19378, 0.15198, -0.16990,
+ -0.21261, 0.25305, -0.15052, -0.29838, 0.01516,
+ 0.10262, 0.01389, -0.22288, -0.04456, 0.39365,
+ 0.22066, -0.01083, 0.65470, -0.12093, -0.15070,
+ 0.21455, 0.56648, 0.12597, -0.23143, 0.11888,
+ -0.46426, -0.09862, 0.13140, 0.21949, -0.29831,
+ -0.34332, -0.00812, -0.46441, -0.23974, 0.05978,
+ 0.03149, -0.13109, 0.07994, 0.11517, 0.29942,
+ 0.40427, 0.08996, 0.31312, -0.20812, 0.16350,
+ -0.18706, -0.79565, -0.18011, -0.17883, 0.37773,
+ -0.36710, -0.37294, 0.29784, -0.17094, -0.28028,
+ 0.24355, 0.25499, -0.35694, -0.06394, -0.11914,
+ 0.12393, 0.44450, -0.03468, 0.42883, -0.17319,
+ -0.46406, -0.36115, -0.48482, -0.03731, -0.03957,
+ 0.36224, -0.07200, -0.25986, -0.09011, -0.02605,
+ -0.10466, 0.48979, -0.00883, 0.01261, -0.00836,
+ -0.29771, 0.18820, 0.38968, -0.43535, 0.28296,
+ -0.06020, -0.28050, -0.02272, 0.00109, 0.32960,
+ -0.08347, -0.06279, 0.32435, -0.37338, -0.41307,
+ 0.01295, -0.36921, 0.11393, -0.28611, 0.07138,
+ 0.12394, 0.08964, 0.48358, -0.09326, -0.13303,
+ 0.20367, -0.11929, 0.48082, -0.07835, -0.02174,
+ -0.07147, 0.32668, -0.87041, -0.24718, 0.10081,
+ 0.24980, -0.09625, -0.13182, 0.08441, 0.03426,
+ 0.17541, -0.08597, -0.09013, 0.06662, -0.07120,
+ -0.30119, 0.35298, 0.17999, 0.18341, 0.01606,
+ -0.27907, -0.07717, 0.38330, -0.38066, 0.11297,
+ -0.08982, 0.19324, -0.33929, 0.10000, 0.21137,
+ 0.07494, 0.02798, -0.37280, 0.25975, -0.25277,
+ 0.35741, 0.19221, 0.42917, 0.33827, -0.13889,
+ -0.03620, -0.78935, -0.52607, -0.04910, -0.04805,
+ -0.01694, 0.32542, 0.30245, -0.57510, -0.27646,
+ -0.15747, -0.34020, -0.16499, 0.30222, 0.47320,
+ 0.14866, 0.15471, 0.51372, 0.50338, -0.45857,
+ -0.13621, -0.34341, -0.06799, -0.41725, 0.17084,
+ -0.25349, 0.01882, 0.21774, 0.13052, 0.01788,
+ -0.14597, 0.13138, -0.04373, 0.09521, 0.50095,
+ 0.37700, 0.89621, 0.49172, -0.11753, 0.37117,
+ -0.75916, 0.16201, 0.02446, -0.29425, -0.47971,
+ -0.10720, -0.03733, 0.31470, -0.30765, 0.43636,
+ -0.27418, -0.43802, -0.43347, -0.72519, 0.29684,
+ -0.05096, 0.40856, 0.40438, 0.13553, -0.16861,
+ 0.69881, 0.02718, 0.21688, -0.18118, -0.45088,
+ -0.30003, 0.21784, 0.29246, -0.19737, -0.03581,
+ 0.22491, -0.59115, 0.08972, 0.02958, -0.41896,
+ -0.86221, 0.11372, 0.41026, 0.49378, 0.15740,
+ -0.13520, 0.06733, 0.18699, 0.30469, 0.14184,
+ -0.09095, -0.24346, 0.62508, -0.00515, 0.36211,
+ 0.33129, 0.35171, -0.09984, -0.41961, -0.76431,
+ 0.18156, -0.59615, -0.16497, 0.53980, 0.24612,
+ 0.21439, -0.34127, -0.24003, -0.19481, 0.07899,
+ 0.23553, -0.46898, -0.06630, -0.08814, 0.18692,
+ 0.49633, 0.33263, -0.06886, 0.13917, -0.01824,
+ -0.22183, -0.46952, -0.11834, -0.08294, 0.48130,
+ 0.04751, 0.37507, -0.08705, 0.14534, -0.55801,
+ -0.10612, 0.18874, -0.55647, -0.00935, 0.02808,
+ 0.16439, 0.15830, 0.58571, 0.41556, -0.49864,
+ 0.08721, 0.47317, 0.09566, -0.43963, 0.27941,
+ -0.09004, 0.27001, -0.19435, -0.05256, 0.22075,
+ -0.17866, 0.03535, -0.17646, -0.43031, -0.18184,
+ 0.62363, 0.14677, 0.12367, 0.16406, 0.38126,
+ -0.14317, -0.11889, 0.33179, 0.02545, -0.62121,
+ 0.35014, 0.24432, 0.03750, -0.28224, -0.29251,
+ 0.02124, -0.28605, 0.17209, -0.55389, -0.25735,
+ 0.00371, 0.29229, 0.21493, -0.40967, -0.02396,
+ 0.54228, -0.05978, 0.01458, 0.07402, 0.38914,
+ 0.29463, 0.01763, 0.45704, 0.40376, -0.37089,
+ -0.03463, -0.03213, 0.09178, 0.30003, -0.23966,
+ -0.54605, -0.25175, 0.37279, 0.02612, -0.22977,
+ -0.17093, -0.04378, 0.15033, -0.33765, -0.03212,
+ -0.32066, 0.12591, -0.16966, 0.44554, 0.53284,
+ 0.04495, 0.15214, 0.05189, -0.31995, 0.17341,
+ 0.38948, -0.17217, -0.67832, 0.50896, -0.02570,
+ -0.38293, -0.07926, -0.29807, -0.24334, 0.31696,
+ -0.30090, 0.09894, 0.20320, 0.25191, 0.07438,
+ 0.42178, -0.09893, -0.09877, 0.40290, -0.27606,
+ 0.30997, -0.00669, -0.51878, -0.32763, -0.25386,
+ 0.33679, 0.30732, -0.28018, -0.44770, -0.31559,
+ -0.15328, 0.33993, 0.04424, -0.06439, -0.00348,
+ 0.37600, -0.50876, -0.18814, -0.25595, 0.17210,
+ -0.51328, 0.19866, 0.39207, -0.24173, -0.03802,
+ 0.31572, 0.12736, -0.10481, -0.00648, 0.36847,
+ -0.51666, -0.58237, -0.30694, 0.08957, 0.18102,
+ 0.04164, 0.27374, -0.26180, -0.15935, -0.06451,
+ 0.69592, 0.03831, -0.03462, -0.19021, 0.11747,
+ 0.16038, 0.02727, -0.59916, -0.35490, 0.05299,
+ -0.14847, 0.04215, 0.08239, 0.22456, 0.14223,
+ -0.04519, 0.39412, 0.18889, -0.03244, 0.18476,
+ 0.18426, 0.12842, -0.15521, -0.20156, 0.24572,
+ 0.06683, -0.03707, -0.05652, -0.67263, -0.18862,
+ -0.07387, -0.21356, 0.06880, 0.13183, 0.01942,
+ 0.24981, 0.09844, -0.79896, 0.31142, 0.24740,
+ 0.22391, 0.12741, -0.35286, -0.25972, -0.06897,
+ 0.52258, -0.32349, -0.06915, 0.04990, 0.25029,
+ 0.35704, 0.09523, -0.13814, -0.48609, 0.22404,
+ -0.08027, 0.19154, -0.24700, 0.01039, 0.50679,
+ -0.26877, -0.15311, 0.26237, -0.23230, 0.02989,
+ -0.02671, 0.26948, -0.75152, -0.22036, -0.13706,
+ 0.24827, 0.20441, -0.02095, 0.15206, -0.18064,
+ 0.12387, 0.13755, 0.23178, 0.06451, -0.11909,
+ -0.24130, -0.24275, -0.02923, 0.25926, 0.04086,
+ -0.47312, 0.00131, 0.25525, 0.12687, 0.00988,
+ -0.25256, -0.52021, 0.00965, -0.04092, 0.00624,
+ 0.28421, 0.52196, 0.19701, 0.03977, 0.11880,
+ 0.19929, 0.00554, -0.70335, 0.17961, -0.00973,
+ 0.20462, -0.15146, 0.10843, 0.42299, -0.06892,
+ 0.30154, -0.12944, -0.08062, -0.28614, -0.07943,
+ 0.04250, -0.48800, 0.68850, -0.41522, 0.14926,
+ -0.16478, 0.45683, 0.37224, -0.25656, 0.39639,
+ -0.06430, 0.68381, -0.34520, 0.12662, 0.47695,
+ -0.19775, 0.09347, -0.01723, -0.16793, -0.12217,
+ 0.15697, 0.31166, -0.86711, -0.28447, 0.16817,
+ 2.10481, -3.77146, 2.48087, -1.39539, -3.93069,
+ -0.96399, -2.10634, 3.76779, -2.49178, 1.38723,
+ 3.93070, 0.97627,
+};
--- /dev/null
+# Copyright 2000-2001 by Andrew Dalke.
+# Revisions copyright 2008 by Peter Cock.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Standard nucleotide and protein alphabets defined by IUPAC."""
+
+from Bio import Alphabet
+from Bio.Data import IUPACData
+
+##################### Protein
+
+# From the IUPAC definition at:
+# http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21
+
+assert IUPACData.extended_protein_letters == IUPACData.extended_protein_letters.upper()
+class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
+ """Extended uppercase IUPAC protein single letter alphabet including X etc.
+
+ In addition to the standard 20 single letter protein codes, this includes:
+
+ B = "Asx"; Aspartic acid (R) or Asparagine (N)
+ X = "Xxx"; Unknown or 'other' amino acid
+ Z = "Glx"; Glutamic acid (E) or Glutamine (Q)
+ J = "Xle"; Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
+ U = "Sec"; Selenocysteine
+ O = "Pyl"; Pyrrolysine
+
+ This alphabet is not intended to be used with X for Selenocysteine
+ (an ad-hoc standard prior to the IUPAC adoption of U instead).
+ """
+ letters = IUPACData.extended_protein_letters
+
+extended_protein = ExtendedIUPACProtein()
+
+assert IUPACData.protein_letters == IUPACData.protein_letters.upper()
+class IUPACProtein(ExtendedIUPACProtein):
+ """Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids."""
+ letters = IUPACData.protein_letters
+
+protein = IUPACProtein()
+
+##################### DNA
+
+# The next two are the IUPAC definitions, from:
+# http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html
+class IUPACAmbiguousDNA(Alphabet.DNAAlphabet):
+ """Uppercase IUPAC ambiguous DNA."""
+ letters = IUPACData.ambiguous_dna_letters
+
+ambiguous_dna = IUPACAmbiguousDNA()
+
+class IUPACUnambiguousDNA(IUPACAmbiguousDNA):
+ """Uppercase IUPAC unambiguous DNA (letters GATC only)."""
+ letters = IUPACData.unambiguous_dna_letters
+
+unambiguous_dna = IUPACUnambiguousDNA()
+
+
+# Also from the URL, but not part of the standard
+class ExtendedIUPACDNA(Alphabet.DNAAlphabet):
+ """Extended IUPAC DNA alphabet.
+
+ In addition to the standard letter codes GATC, this includes:
+
+ B = 5-bromouridine
+ D = 5,6-dihydrouridine
+ S = thiouridine
+ W = wyosine
+ """
+ letters = IUPACData.extended_dna_letters
+
+extended_dna = ExtendedIUPACDNA()
+
+##################### RNA
+
+class IUPACAmbiguousRNA(Alphabet.RNAAlphabet):
+ """Uppercase IUPAC ambiguous RNA."""
+ letters = IUPACData.ambiguous_rna_letters
+
+ambiguous_rna = IUPACAmbiguousRNA()
+
+class IUPACUnambiguousRNA(IUPACAmbiguousRNA):
+ """Uppercase IUPAC unambiguous RNA (letters GAUC only)."""
+ letters = IUPACData.unambiguous_rna_letters
+
+unambiguous_rna = IUPACUnambiguousRNA()
+
+# are there extended forms?
+#class ExtendedIUPACRNA(Alphabet.RNAAlphabet):
+# letters = extended_rna_letters
+# # B == 5-bromouridine
+# # D == 5,6-dihydrouridine
+# # S == thiouridine
+# # W == wyosine
+
+
+# We need to load the property resolution information, but we need to
+# wait until after the systems have been loaded. (There's a nasty loop
+# where, eg, translation objects need an alphabet, which need to be
+# assocated with translators.)
+
+from Bio.PropertyManager import default_manager
+
+def _bootstrap(manager, klass, property):
+ assert manager is default_manager
+ del default_manager.class_resolver[IUPACProtein]
+ del default_manager.class_resolver[ExtendedIUPACProtein]
+ del default_manager.class_resolver[IUPACAmbiguousDNA]
+ del default_manager.class_resolver[IUPACUnambiguousDNA]
+ del default_manager.class_resolver[ExtendedIUPACDNA]
+ del default_manager.class_resolver[IUPACAmbiguousRNA]
+ del default_manager.class_resolver[IUPACUnambiguousRNA]
+
+ from Bio.Encodings import IUPACEncoding
+
+ return manager.resolve_class(klass, property)
+
+default_manager.class_resolver[IUPACProtein] = _bootstrap
+default_manager.class_resolver[ExtendedIUPACProtein] = _bootstrap
+default_manager.class_resolver[IUPACAmbiguousDNA] = _bootstrap
+default_manager.class_resolver[IUPACUnambiguousDNA] = _bootstrap
+default_manager.class_resolver[ExtendedIUPACDNA] = _bootstrap
+default_manager.class_resolver[IUPACAmbiguousRNA] = _bootstrap
+default_manager.class_resolver[IUPACUnambiguousRNA] = _bootstrap
--- /dev/null
+# Copyright 2004 by Iddo Friedberg.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Reduced alphabets which lump together several amino-acids into one letter.
+
+Reduced (redundant or simplified) alphabets are used to represent protein sequences using an
+alternative alphabet which lumps together several amino-acids into one letter, based
+on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually
+quite interchangeable, so many sequence studies group them into one letter
+
+Examples of reduced alphabets are available in:
+
+http://viscose.ifg.uni-muenster.de/html/alphabets.html
+
+Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of
+the tables here, or a user-defined table.
+"""
+
+from Bio import Alphabet
+
+# The Murphy tables are from here:
+# Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid alphabets for protein
+# fold recognition and implications for folding. Protein Eng. 13(3):149-152
+
+murphy_15_tab = {"L": "L",
+ "V": "L",
+ "I": "L",
+ "M": "L",
+ "C": "C",
+ "A": "A",
+ "G": "G",
+ "S": "S",
+ "T": "T",
+ "P": "P",
+ "F": "F",
+ "Y": "F",
+ "W": "W",
+ "E": "E",
+ "D": "D",
+ "N": "N",
+ "Q": "Q",
+ "K": "K",
+ "R": "K",
+ "H": "H"}
+
+class Murphy15(Alphabet.ProteinAlphabet):
+ letters = "LCAGSTPFWEDNQKH"
+ size = 15
+murphy_15 = Murphy15()
+
+murphy_10_tab = {"L": "L",
+ "V": "L",
+ "I": "L",
+ "M": "L",
+ "C": "C",
+ "A": "A",
+ "G": "G",
+ "S": "S",
+ "T": "S",
+ "P": "P",
+ "F": "F",
+ "Y": "F",
+ "W": "F",
+ "E": "E",
+ "D": "E",
+ "N": "E",
+ "Q": "E",
+ "K": "K",
+ "R": "K",
+ "H": "H"}
+class Murphy10(Alphabet.ProteinAlphabet):
+ letters = "LCAGSPFEKH"
+ size = 10
+murphy_10 = Murphy10()
+
+murphy_8_tab = {"L": "L",
+ "V": "L",
+ "I": "L",
+ "M": "L",
+ "C": "L",
+ "A": "A",
+ "G": "A",
+ "S": "S",
+ "T": "S",
+ "P": "P",
+ "F": "F",
+ "Y": "F",
+ "W": "F",
+ "E": "E",
+ "D": "E",
+ "N": "E",
+ "Q": "E",
+ "K": "K",
+ "R": "K",
+ "H": "H"}
+
+class Murphy8(Alphabet.ProteinAlphabet):
+ letters = "LASPFEKH"
+ size = 8
+murphy_8 = Murphy8()
+
+murphy_4_tab = {"L": "L",
+ "V": "L",
+ "I": "L",
+ "M": "L",
+ "C": "L",
+ "A": "A",
+ "G": "A",
+ "S": "A",
+ "T": "A",
+ "P": "A",
+ "F": "F",
+ "Y": "F",
+ "W": "F",
+ "E": "E",
+ "D": "E",
+ "N": "E",
+ "Q": "E",
+ "K": "E",
+ "R": "E",
+ "H": "E"}
+
+class Murphy4(Alphabet.ProteinAlphabet):
+ letters = "LAFE"
+ size = 4
+murphy_4 = Murphy4()
+
+hp_model_tab = {"A": "P", # Hydrophilic
+ "G": "P",
+ "T": "P",
+ "S": "P",
+ "N": "P",
+ "Q": "P",
+ "D": "P",
+ "E": "P",
+ "H": "P",
+ "R": "P",
+ "K": "P",
+ "P": "P",
+ "C": "H", # Hydrophobic
+ "M": "H",
+ "F": "H",
+ "I": "H",
+ "L": "H",
+ "V": "H",
+ "W": "H",
+ "Y": "H"}
+
+class HPModel(Alphabet.ProteinAlphabet):
+ letters = "HP"
+ size = 2
+hp_model = HPModel()
+
+pc_5_table = {"I": "A", # Aliphatic
+ "V": "A",
+ "L": "A",
+ "F": "R", # Aromatic
+ "Y": "R",
+ "W": "R",
+ "H": "R",
+ "K": "C", # Charged
+ "R": "C",
+ "D": "C",
+ "E": "C",
+ "G": "T", # Tiny
+ "A": "T",
+ "C": "T",
+ "S": "T",
+ "T": "D", # Diverse
+ "M": "D",
+ "Q": "D",
+ "N": "D",
+ "P": "D"}
+
+class PC5(Alphabet.ProteinAlphabet):
+ letters = "ARCTD"
+ size = 5
+hp_model = HPModel()
--- /dev/null
+# Copyright 2000-2002 by Andrew Dalke.
+# Revisions copyright 2007-2008 by Peter Cock.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Alphabets used in Seq objects etc to declare sequence type and letters.
+
+This is used by sequences which contain a finite number of similar words.
+"""
+
+class Alphabet:
+ size = None # no fixed size for words
+ letters = None # no fixed alphabet; implement as a list-like
+ # interface,
+ def __repr__(self):
+ return self.__class__.__name__ + "()"
+
+ def contains(self, other):
+ """Does this alphabet 'contain' the other (OBSOLETE?).
+
+ Returns a boolean. This relies on the Alphabet subclassing
+ hierarchy only, and does not check the letters property.
+ This isn't ideal, and doesn't seem to work as intended
+ with the AlphabetEncoder classes."""
+ return isinstance(other, self.__class__)
+
+generic_alphabet = Alphabet()
+
+class SingleLetterAlphabet(Alphabet):
+ size = 1
+ letters = None # string of all letters in the alphabet
+
+single_letter_alphabet = SingleLetterAlphabet()
+
+########### Protein
+
+class ProteinAlphabet(SingleLetterAlphabet):
+ pass
+
+generic_protein = ProteinAlphabet()
+
+########### DNA
+class NucleotideAlphabet(SingleLetterAlphabet):
+ pass
+
+generic_nucleotide = NucleotideAlphabet()
+
+class DNAAlphabet(NucleotideAlphabet):
+ pass
+
+generic_dna = DNAAlphabet()
+
+
+########### RNA
+
+class RNAAlphabet(NucleotideAlphabet):
+ pass
+
+generic_rna = RNAAlphabet()
+
+
+
+########### Other per-sequence encodings
+
+class SecondaryStructure(SingleLetterAlphabet):
+ letters = "HSTC"
+
+class ThreeLetterProtein(Alphabet):
+ size = 3
+ letters = [
+ "Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
+ "Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr",
+ "Sec", "Val", "Trp", "Xaa", "Tyr", "Glx",
+ ]
+
+###### Non per-sequence modifications
+
+# (These are Decorator classes)
+
+class AlphabetEncoder:
+ def __init__(self, alphabet, new_letters):
+ self.alphabet = alphabet
+ self.new_letters = new_letters
+ if alphabet.letters is not None:
+ self.letters = alphabet.letters + new_letters
+ else:
+ self.letters = None
+ def __getattr__(self, key):
+ if key[:2] == "__" and key[-2:] == "__":
+ raise AttributeError(key)
+ return getattr(self.alphabet, key)
+
+ def __repr__(self):
+ return "%s(%r, %r)" % (self.__class__.__name__, self.alphabet,
+ self.new_letters)
+
+ def contains(self, other):
+ """Does this alphabet 'contain' the other (OBSOLETE?).
+
+ This is isn't implemented for the base AlphabetEncoder,
+ which will always return 0 (False)."""
+ return 0
+
+class Gapped(AlphabetEncoder):
+ def __init__(self, alphabet, gap_char = "-"):
+ AlphabetEncoder.__init__(self, alphabet, gap_char)
+ self.gap_char = gap_char
+
+ def contains(self, other):
+ """Does this alphabet 'contain' the other (OBSOLETE?).
+
+ Returns a boolean. This relies on the Alphabet subclassing
+ hierarchy, and attempts to check the gap character. This fails
+ if the other alphabet does not have a gap character!
+ """
+ return other.gap_char == self.gap_char and \
+ self.alphabet.contains(other.alphabet)
+
+class HasStopCodon(AlphabetEncoder):
+ def __init__(self, alphabet, stop_symbol = "*"):
+ AlphabetEncoder.__init__(self, alphabet, stop_symbol)
+ self.stop_symbol = stop_symbol
+
+ def __cmp__(self, other):
+ x = cmp(self.alphabet, other.alphabet)
+ if x == 0:
+ return cmp(self.stop_symbol, other.stop_symbol)
+ return x
+
+ def contains(self, other):
+ """Does this alphabet 'contain' the other (OBSOLETE?).
+
+ Returns a boolean. This relies on the Alphabet subclassing
+ hierarchy, and attempts to check the stop symbol. This fails
+ if the other alphabet does not have a stop symbol!
+ """
+ return other.stop_symbol == self.stop_symbol and \
+ self.alphabet.contains(other.alphabet)
+
+def _get_base_alphabet(alphabet) :
+ """Returns the non-gapped non-stop-codon Alphabet object (PRIVATE)."""
+ a = alphabet
+ while isinstance(a, AlphabetEncoder) :
+ a = a.alphabet
+ assert isinstance(a, Alphabet), \
+ "Invalid alphabet found, %s" % repr(a)
+ return a
+
+def _consensus_base_alphabet(alphabets) :
+ """Returns a common but often generic base alphabet object (PRIVATE).
+
+ This throws away any AlphabetEncoder information, e.g. Gapped alphabets.
+
+ Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
+ letter. These DO NOT raise an exception!"""
+ common = None
+ for alpha in alphabets :
+ a = _get_base_alphabet(alpha)
+ if common is None :
+ common = a
+ elif common == a :
+ pass
+ elif isinstance(a, common.__class__) :
+ pass
+ elif isinstance(common, a.__class__) :
+ common = a
+ elif isinstance(a, NucleotideAlphabet) \
+ and isinstance(common, NucleotideAlphabet) :
+ #e.g. Give a mix of RNA and DNA alphabets
+ common = generic_nucleotide
+ elif isinstance(a, SingleLetterAlphabet) \
+ and isinstance(common, SingleLetterAlphabet) :
+ #This is a pretty big mis-match!
+ common = single_letter_alphabet
+ else :
+ #We have a major mis-match... take the easy way out!
+ return generic_alphabet
+ if common is None :
+ #Given NO alphabets!
+ return generic_alphabet
+ return common
+
+def _consensus_alphabet(alphabets) :
+ """Returns a common but often generic alphabet object (PRIVATE).
+
+ Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
+ letter. These DO NOT raise an exception!
+
+ This is aware of Gapped and HasStopCodon and new letters added by
+ other AlphabetEncoders. This WILL raise an exception if more than
+ one gap character or stop symbol is present."""
+ base = _consensus_base_alphabet(alphabets)
+ gap = None
+ stop = None
+ new_letters = ""
+ for alpha in alphabets :
+ #Gaps...
+ if not hasattr(alpha, "gap_char") :
+ pass
+ elif gap is None :
+ gap = alpha.gap_char
+ elif gap == alpha.gap_char :
+ pass
+ else :
+ raise ValueError("More than one gap character present")
+ #Stops...
+ if not hasattr(alpha, "stop_symbol") :
+ pass
+ elif stop is None :
+ stop = alpha.stop_symbol
+ elif stop == alpha.stop_symbol :
+ pass
+ else :
+ raise ValueError("More than one stop symbol present")
+ #New letters...
+ if hasattr(alpha, "new_letters") :
+ for letter in alpha.new_letters :
+ if letter not in new_letters \
+ and letter != gap and letter != stop :
+ new_letters += letter
+
+ alpha = base
+ if new_letters :
+ alpha = AlphabetEncoder(alpha, new_letters)
+ if gap :
+ alpha = Gapped(alpha, gap_char=gap)
+ if stop :
+ alpha = HasStopCodon(alpha, stop_symbol=stop)
+ return alpha
+
+def _check_type_compatible(alphabets) :
+ """Returns True except for DNA+RNA or Nucleotide+Protein (PRIVATE).
+
+ This relies on the Alphabet subclassing hierarchy. It does not
+ check things like gap characters or stop symbols."""
+ dna, rna, nucl, protein = False, False, False, False
+ for alpha in alphabets :
+ a = _get_base_alphabet(alpha)
+ if isinstance(a, DNAAlphabet) :
+ dna = True
+ nucl = True
+ if rna or protein : return False
+ elif isinstance(a, RNAAlphabet) :
+ rna = True
+ nucl = True
+ if dna or protein : return False
+ elif isinstance(a, NucleotideAlphabet) :
+ nucl = True
+ if protein : return False
+ elif isinstance(a, ProteinAlphabet) :
+ protein = True
+ if nucl : return False
+ return True
--- /dev/null
+"""General mechanisms to access applications in biopython.
+"""
+import os, sys
+import StringIO
+
+from Bio import File
+
+def generic_run(commandline):
+ """Run an application with the given commandline.
+
+ This expects a pre-built commandline that derives from
+ AbstractCommandline, and returns a ApplicationResult object
+ to get results from a program, along with handles of the
+ standard output and standard error.
+
+ WARNING - This will read in the full program output into memory!
+ This may be in issue when the program write a large amount of
+ data to standard output.
+ """
+ # print str(commandline)
+
+ #Try and use subprocess (available in python 2.4+)
+ try :
+ import subprocess, sys
+ #We don't need to supply any piped input, but we setup the
+ #standard input pipe anyway as a work around for a python
+ #bug if this is called from a Windows GUI program. For
+ #details, see http://bugs.python.org/issue1124861
+ child = subprocess.Popen(str(commandline),
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ shell=(sys.platform!="win32"))
+ child.stdin.close()
+ r = child.stdout
+ e = child.stderr
+
+ r_out = r.read()
+ e_out = e.read()
+ r.close()
+ e.close()
+
+ # capture error code
+ error_code = child.wait()
+
+ except ImportError :
+ #For python 2.3 can't use subprocess, using popen2 instead
+ #(deprecated in python 2.6)
+ import popen2
+ if sys.platform[:3]=='win':
+ # Windows does not have popen2.Popen3
+ r, w, e = popen2.popen3(str(commandline))
+
+ r_out = r.read()
+ e_out = e.read()
+ w.close()
+ r.close()
+ e.close()
+
+ # No way to get the error code; setting it to a dummy variable
+ error_code = 0
+
+ else:
+ child = popen2.Popen3(str(commandline), 1)
+ # get information and close the files, so if we call this function
+ # repeatedly we won't end up with too many open files
+
+ # here are the file descriptors
+ r = child.fromchild
+ w = child.tochild
+ e = child.childerr
+
+ r_out = r.read()
+ e_out = e.read()
+ w.close()
+ r.close()
+ e.close()
+
+ # capture error code
+ error_code = os.WEXITSTATUS(child.wait())
+
+ return ApplicationResult(commandline, error_code), \
+ File.UndoHandle(StringIO.StringIO(r_out)), \
+ File.UndoHandle(StringIO.StringIO(e_out))
+
+class ApplicationResult:
+ """Make results of a program available through a standard interface.
+
+ This tries to pick up output information available from the program
+ and make it available programmatically.
+ """
+ def __init__(self, application_cl, return_code):
+ """Intialize with the commandline from the program.
+ """
+ self._cl = application_cl
+
+ # provide the return code of the application
+ self.return_code = return_code
+
+ # get the application dependent results we can provide
+ # right now the only results we handle are output files
+ self._results = {}
+
+ for parameter in self._cl.parameters:
+ if "file" in parameter.param_types and \
+ "output" in parameter.param_types:
+ if parameter.is_set:
+ self._results[parameter.names[-1]] = parameter.value
+
+ def get_result(self, output_name):
+ """Retrieve result information for the given output.
+ """
+ return self._results[output_name]
+
+ def available_results(self):
+ """Retrieve a list of all available results.
+ """
+ result_names = self._results.keys()
+ result_names.sort()
+ return result_names
+
+class AbstractCommandline:
+ """Generic interface for running applications from biopython.
+
+ This class shouldn't be called directly; it should be subclassed to
+ provide an implementation for a specific application.
+ """
+ def __init__(self):
+ self.program_name = ""
+ self.parameters = []
+
+ def __str__(self):
+ """Make the commandline with the currently set options.
+ """
+ commandline = "%s " % self.program_name
+ for parameter in self.parameters:
+ if parameter.is_required and not(parameter.is_set):
+ raise ValueError("Parameter %s is not set." % parameter.names)
+ if parameter.is_set:
+ commandline += str(parameter)
+
+ return commandline
+
+ def set_parameter(self, name, value = None):
+ """Set a commandline option for a program.
+ """
+ set_option = 0
+ for parameter in self.parameters:
+ if name in parameter.names:
+ if value is not None:
+ self._check_value(value, name, parameter.checker_function)
+ parameter.value = value
+ parameter.is_set = 1
+ set_option = 1
+
+ if set_option == 0:
+ raise ValueError("Option name %s was not found." % name)
+
+ def _check_value(self, value, name, check_function):
+ """Check whether the given value is valid.
+
+ This uses the passed function 'check_function', which can either
+ return a [0, 1] (bad, good) value or raise an error. Either way
+ this function will raise an error if the value is not valid, or
+ finish silently otherwise.
+ """
+ if check_function is not None:
+ is_good = check_function(value)
+ if is_good in [0, 1]: # if we are dealing with a good/bad check
+ if not(is_good):
+ raise ValueError(
+ "Invalid parameter value %r for parameter %s" %
+ (value, name))
+
+class _AbstractParameter:
+ """A class to hold information about a parameter for a commandline.
+
+ Do not use this directly, instead use one of the subclasses.
+
+ Attributes:
+
+ o names -- a list of string names by which the parameter can be
+ referenced (ie. ["-a", "--append", "append"]). The first name in
+ the list is considered to be the one that goes on the commandline,
+ for those parameters that print the option. The last name in the list
+ is assumed to be a "human readable" name describing the option in one
+ word.
+
+ o param_type -- a list of string describing the type of parameter,
+ which can help let programs know how to use it. Example descriptions
+ include 'input', 'output', 'file'
+
+ o checker_function -- a reference to a function that will determine
+ if a given value is valid for this parameter. This function can either
+ raise an error when given a bad value, or return a [0, 1] decision on
+ whether the value is correct.
+
+ o description -- a description of the option.
+
+ o is_required -- a flag to indicate if the parameter must be set for
+ the program to be run.
+
+ o is_set -- if the parameter has been set
+
+ o value -- the value of a parameter
+ """
+ def __init__(self, names = [], types = [], checker_function = None,
+ is_required = 0, description = ""):
+ self.names = names
+ self.param_types = types
+ self.checker_function = checker_function
+ self.description = description
+ self.is_required = is_required
+
+ self.is_set = 0
+ self.value = None
+
+class _Option(_AbstractParameter):
+ """Represent an option that can be set for a program.
+
+ This holds UNIXish options like --append=yes and -a yes
+ """
+ def __str__(self):
+ """Return the value of this option for the commandline.
+ """
+ # first deal with long options
+ if self.names[0].find("--") >= 0:
+ output = "%s" % self.names[0]
+ if self.value is not None:
+ output += "=%s " % self.value
+ else:
+ output += " "
+ # now short options
+ elif self.names[0].find("-") >= 0:
+ output = "%s " % self.names[0]
+ if self.value is not None:
+ output += "%s " % self.value
+ else:
+ raise ValueError("Unrecognized option type: %s" % self.names[0])
+
+ return output
+
+class _Argument(_AbstractParameter):
+ """Represent an argument on a commandline.
+ """
+ def __str__(self):
+ if self.value is not None:
+ return "%s " % self.value
+ else:
+ return " "
--- /dev/null
+#TODO - Remove this work around once we drop python 2.3 support
+try:
+ set = set
+except NameError:
+ from sets import Set as set
+
+from Bio import Alphabet
+from Bio.Alphabet import IUPAC
+from Bio.Data import IUPACData
+
+unambiguous_dna_by_name = {}
+unambiguous_dna_by_id = {}
+unambiguous_rna_by_name = {}
+unambiguous_rna_by_id = {}
+generic_by_name = {} # unambiguous DNA or RNA
+generic_by_id = {} # unambiguous DNA or RNA
+ambiguous_generic_by_name = {} # ambiguous DNA or RNA
+ambiguous_generic_by_id = {} # ambiguous DNA or RNA
+
+# standard IUPAC unambiguous codons
+standard_dna_table = None
+standard_rna_table = None
+
+# In the future, the back_table could return a statistically
+# appropriate distribution of codons, so do not cache the results of
+# back_table lookups!
+
+class TranslationError(Exception):
+ pass
+
+class CodonTable:
+ nucleotide_alphabet = Alphabet.generic_nucleotide
+ protein_alphabet = Alphabet.generic_protein
+
+ forward_table = {} # only includes codons which actually code
+ back_table = {} # for back translations
+ start_codons = []
+ stop_codons = []
+ # Not always called from derived classes!
+ def __init__(self, nucleotide_alphabet = nucleotide_alphabet,
+ protein_alphabet = protein_alphabet,
+ forward_table = forward_table, back_table = back_table,
+ start_codons = start_codons, stop_codons = stop_codons):
+ self.nucleotide_alphabet = nucleotide_alphabet
+ self.protein_alphabet = protein_alphabet
+ self.forward_table = forward_table
+ self.back_table = back_table
+ self.start_codons = start_codons
+ self.stop_codons = stop_codons
+
+ def __str__(self) :
+ """Returns a simple text representation of the codon table
+
+ e.g.
+ >>> import Bio.Data.CodonTable
+ >>> print Bio.Data.CodonTable.standard_dna_table
+ >>> print Bio.Data.CodonTable.generic_by_id[1]"""
+
+ if self.id :
+ answer = "Table %i" % self.id
+ else :
+ answer = "Table ID unknown"
+ if self.names :
+ answer += " " + ", ".join(filter(None, self.names))
+
+ #Use the main four letters (and the conventional ordering)
+ #even for ambiguous tables
+ letters = self.nucleotide_alphabet.letters
+ if isinstance(self.nucleotide_alphabet, Alphabet.DNAAlphabet) \
+ or (letters is not None and "T" in letters) :
+ letters = "TCAG"
+ else :
+ #Should be either RNA or generic nucleotides,
+ #e.g. Bio.Data.CodonTable.generic_by_id[1]
+ letters = "UCAG"
+
+ #Build the table...
+ answer=answer + "\n\n |" + "|".join( \
+ [" %s " % c2 for c2 in letters] \
+ ) + "|"
+ answer=answer + "\n--+" \
+ + "+".join(["---------" for c2 in letters]) + "+--"
+ for c1 in letters :
+ for c3 in letters :
+ line = c1 + " |"
+ for c2 in letters :
+ codon = c1+c2+c3
+ line = line + " %s" % codon
+ if codon in self.stop_codons :
+ line = line + " Stop|"
+ else :
+ try :
+ amino = self.forward_table[codon]
+ except KeyError :
+ amino = "?"
+ except TranslationError :
+ amino = "?"
+ if codon in self.start_codons :
+ line = line + " %s(s)|" % amino
+ else :
+ line = line + " %s |" % amino
+ line = line + " " + c3
+ answer = answer + "\n"+ line
+ answer=answer + "\n--+" \
+ + "+".join(["---------" for c2 in letters]) + "+--"
+ return answer
+
+def make_back_table(table, default_stop_codon):
+ # ONLY RETURNS A SINGLE CODON
+ # Do the sort so changes in the hash implementation won't affect
+ # the result when one amino acid is coded by more than one codon.
+ back_table = {}
+ keys = table.keys() ; keys.sort()
+ for key in keys:
+ back_table[table[key]] = key
+ back_table[None] = default_stop_codon
+ return back_table
+
+
+class NCBICodonTable(CodonTable):
+ nucleotide_alphabet = Alphabet.generic_nucleotide
+ protein_alphabet = IUPAC.protein
+
+ def __init__(self, id, names, table, start_codons, stop_codons):
+ self.id = id
+ self.names = names
+ self.forward_table = table
+ self.back_table = make_back_table(table, stop_codons[0])
+ self.start_codons = start_codons
+ self.stop_codons = stop_codons
+
+
+class NCBICodonTableDNA(NCBICodonTable):
+ nucleotide_alphabet = IUPAC.unambiguous_dna
+
+class NCBICodonTableRNA(NCBICodonTable):
+ nucleotide_alphabet = IUPAC.unambiguous_rna
+
+
+
+def register_ncbi_table(name, alt_name, id,
+ table, start_codons, stop_codons):
+ names = name.split("; ")
+
+ dna = NCBICodonTableDNA(id, names + [alt_name], table, start_codons,
+ stop_codons)
+ # replace all T's with U's for the RNA tables
+ rna_table = {}
+ generic_table = {}
+ for codon, val in table.items():
+ generic_table[codon] = val
+ codon = codon.replace("T", "U")
+ generic_table[codon] = val
+ rna_table[codon] = val
+ rna_start_codons = []
+ generic_start_codons = []
+ for codon in start_codons:
+ generic_start_codons.append(codon)
+ codon = codon.replace("T", "U")
+ generic_start_codons.append(codon)
+ rna_start_codons.append(codon)
+ rna_stop_codons = []
+ generic_stop_codons = []
+ for codon in stop_codons:
+ generic_stop_codons.append(codon)
+ codon = codon.replace("T", "U")
+ generic_stop_codons.append(codon)
+ rna_stop_codons.append(codon)
+
+ generic = NCBICodonTable(id, names + [alt_name], generic_table,
+ generic_start_codons, generic_stop_codons)
+ rna = NCBICodonTableRNA(id, names + [alt_name], rna_table,
+ rna_start_codons, rna_stop_codons)
+
+ if id == 1:
+ global standard_dna_table, standard_rna_table
+ standard_dna_table = dna
+ standard_rna_table = rna
+
+ unambiguous_dna_by_id[id] = dna
+ unambiguous_rna_by_id[id] = rna
+ generic_by_id[id] = generic
+
+ if alt_name is not None:
+ names.append(alt_name)
+
+ for name in names:
+ unambiguous_dna_by_name[name] = dna
+ unambiguous_rna_by_name[name] = rna
+ generic_by_name[name] = generic
+
+### These tables created from the data file
+### ftp://ncbi.nlm.nih.gov/entrez/misc/data/gc.prt
+### using the following:
+##import re
+##for line in open("gc.prt").readlines():
+## if line[:2] == " {":
+## names = []
+## id = None
+## aa = None
+## start = None
+## bases = []
+## elif line[:6] == " name":
+## names.append(re.search('"([^"]*)"', line).group(1))
+## elif line[:8] == " name":
+## names.append(re.search('"(.*)$', line).group(1))
+## elif line == ' Mitochondrial; Mycoplasma; Spiroplasma" ,\n':
+## names[-1] = names[-1] + " Mitochondrial; Mycoplasma; Spiroplasma"
+## elif line[:4] == " id":
+## id = int(re.search('(\d+)', line).group(1))
+## elif line[:10] == " ncbieaa ":
+## aa = line[12:12+64]
+## elif line[:10] == " sncbieaa":
+## start = line[12:12+64]
+## elif line[:9] == " -- Base":
+## bases.append(line[12:12+64])
+## elif line[:2] == " }":
+## assert names != [] and id is not None and aa is not None
+## assert start is not None and bases != []
+## if len(names) == 1:
+## names.append(None)
+## print "register_ncbi_table(name = %s," % repr(names[0])
+## print " alt_name = %s, id = %d", % \
+## (repr(names[1]), id)
+## print " table = {"
+## s = " "
+## for i in range(64):
+## if aa[i] != "*":
+## t = " '%s%s%s': '%s'," % (bases[0][i], bases[1][i],
+## bases[2][i], aa[i])
+## if len(s) + len(t) > 75:
+## print s
+## s = " " + t
+## else:
+## s = s + t
+## print s, "},"
+
+## s = " stop_codons = ["
+## for i in range(64):
+## if aa[i] == "*":
+## t = " '%s%s%s'," % (bases[0][i], bases[1][i], bases[2][i])
+## if len(s) + len(t) > 75:
+## print s
+## s = " " + t
+## else:
+## s = s + t
+## print s, "],"
+
+## s = " start_codons = ["
+## for i in range(64):
+## if start[i] == "M":
+## t = " '%s%s%s'," % (bases[0][i], bases[1][i], bases[2][i])
+## if len(s) + len(t) > 75:
+## print s
+## s = " " + t
+## else:
+## s = s + t
+## print s, "]"
+## print " )"
+## elif line[:2] == "--" or line == "\n" or line == "}\n" or \
+## line == 'Genetic-code-table ::= {\n':
+## pass
+## else:
+## raise Exception("Unparsed: " + repr(line))
+
+register_ncbi_table(name = 'Standard',
+ alt_name = 'SGC0', id = 1,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L',
+ 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P',
+ 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
+ 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I',
+ 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T',
+ 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K',
+ 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
+ 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A',
+ 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D',
+ 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G',
+ 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', 'TGA', ],
+ start_codons = [ 'TTG', 'CTG', 'ATG', ]
+ )
+register_ncbi_table(name = 'Vertebrate Mitochondrial',
+ alt_name = 'SGC1', id = 2,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'GTT': 'V',
+ 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A',
+ 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E',
+ 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', 'AGA', 'AGG', ],
+ start_codons = [ 'ATT', 'ATC', 'ATA', 'ATG', 'GTG', ]
+ )
+register_ncbi_table(name = 'Yeast Mitochondrial',
+ alt_name = 'SGC2', id = 3,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'T',
+ 'CTC': 'T', 'CTA': 'T', 'CTG': 'T', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R',
+ 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma',
+ alt_name = 'SGC3', id = 4,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R',
+ 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'TTA', 'TTG', 'CTG', 'ATT', 'ATC',
+ 'ATA', 'ATG', 'GTG', ]
+ )
+register_ncbi_table(name = 'Invertebrate Mitochondrial',
+ alt_name = 'SGC4', id = 5,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S',
+ 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'TTG', 'ATT', 'ATC', 'ATA', 'ATG',
+ 'GTG', ]
+ )
+register_ncbi_table(name = 'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear',
+ alt_name = 'SGC5', id = 6,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TAA': 'Q', 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W',
+ 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P',
+ 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H',
+ 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R',
+ 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
+ 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N',
+ 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S',
+ 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V',
+ 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
+ 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G',
+ 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TGA', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Echinoderm Mitochondrial',
+ alt_name = 'SGC8', id = 9,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'N', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S',
+ 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Euplotid Nuclear',
+ alt_name = 'SGC9', id = 10,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'C', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R',
+ 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Bacterial',
+ alt_name = None, id = 11,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L',
+ 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P',
+ 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
+ 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I',
+ 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T',
+ 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K',
+ 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
+ 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A',
+ 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D',
+ 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G',
+ 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', 'TGA', ],
+ start_codons = [ 'TTG', 'CTG', 'ATT', 'ATC', 'ATA',
+ 'ATG', 'GTG', ]
+ )
+register_ncbi_table(name = 'Alternative Yeast Nuclear',
+ alt_name = None, id = 12,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L',
+ 'CTA': 'L', 'CTG': 'S', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P',
+ 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
+ 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I',
+ 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T',
+ 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K',
+ 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
+ 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A',
+ 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D',
+ 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G',
+ 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', 'TGA', ],
+ start_codons = [ 'CTG', 'ATG', ]
+ )
+register_ncbi_table(name = 'Ascidian Mitochondrial',
+ alt_name = None, id = 13,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'G',
+ 'AGG': 'G', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TAG', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Flatworm Mitochondrial',
+ alt_name = None, id = 14,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TAA': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W',
+ 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P',
+ 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H',
+ 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R',
+ 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
+ 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N',
+ 'AAC': 'N', 'AAA': 'N', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S',
+ 'AGA': 'S', 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V',
+ 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
+ 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G',
+ 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAG', ],
+ start_codons = [ 'ATG', ]
+ )
+register_ncbi_table(name = 'Blepharisma Macronuclear',
+ alt_name = None, id = 15,
+ table = {
+ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S',
+ 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y',
+ 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L',
+ 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P',
+ 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q',
+ 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
+ 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T',
+ 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N',
+ 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R',
+ 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
+ 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D',
+ 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G',
+ 'GGA': 'G', 'GGG': 'G', },
+ stop_codons = [ 'TAA', 'TGA', ],
+ start_codons = [ 'ATG', ]
+ )
+
+######### Deal with ambiguous forward translations
+
+class AmbiguousCodonTable(CodonTable):
+ def __init__(self, codon_table,
+ ambiguous_nucleotide_alphabet,
+ ambiguous_nucleotide_values,
+ ambiguous_protein_alphabet,
+ ambiguous_protein_values):
+ CodonTable.__init__(self,
+ ambiguous_nucleotide_alphabet,
+ ambiguous_protein_alphabet,
+ AmbiguousForwardTable(codon_table.forward_table,
+ ambiguous_nucleotide_values,
+ ambiguous_protein_values),
+ codon_table.back_table,
+
+ # These two are WRONG! I need to get the
+ # list of ambiguous codons which code for
+ # the stop codons XXX
+ list_ambiguous_codons(codon_table.start_codons, ambiguous_nucleotide_values),
+ list_ambiguous_codons(codon_table.stop_codons, ambiguous_nucleotide_values)
+ )
+ self._codon_table = codon_table
+
+ # Be sneaky and forward attribute lookups to the original table.
+ # This lets us get the names, if the original table is an NCBI
+ # table.
+ def __getattr__(self, name):
+ return getattr(self._codon_table, name)
+
+def list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values):
+ c1, c2, c3 = codon
+ x1 = ambiguous_nucleotide_values[c1]
+ x2 = ambiguous_nucleotide_values[c2]
+ x3 = ambiguous_nucleotide_values[c3]
+ possible = {}
+ stops = []
+ for y1 in x1:
+ for y2 in x2:
+ for y3 in x3:
+ try:
+ possible[forward_table[y1+y2+y3]] = 1
+ except KeyError:
+ # If tripping over a stop codon
+ stops.append(y1+y2+y3)
+ if stops:
+ if possible.keys():
+ raise TranslationError("ambiguous codon '%s' codes " % codon \
+ + "for both proteins and stop codons")
+ # This is a true stop codon - tell the caller about it
+ raise KeyError(codon)
+ return possible.keys()
+
+def list_ambiguous_codons(codons, ambiguous_nucleotide_values):
+ """Extends a codon list to include all possible ambigous codons.
+
+ e.g. ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR']
+ ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA']
+
+ Note that ['TAG', 'TGA'] -> ['TAG', 'TGA'], this does not add 'TRR'.
+ Thus only two more codons are added in the following:
+
+ e.g. ['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']
+
+ Returns a new (longer) list of codon strings.
+ """
+
+ #Note ambiguous_nucleotide_values['R'] = 'AG' (etc)
+ #This will generate things like 'TRR' from ['TAG', 'TGA'], which
+ #we don't want to include:
+ c1_list = [letter for (letter, meanings) \
+ in ambiguous_nucleotide_values.iteritems() \
+ if set([codon[0] for codon in codons]).issuperset(set(meanings))]
+ c2_list = [letter for (letter, meanings) \
+ in ambiguous_nucleotide_values.iteritems() \
+ if set([codon[1] for codon in codons]).issuperset(set(meanings))]
+ c3_list = [letter for (letter, meanings) \
+ in ambiguous_nucleotide_values.iteritems() \
+ if set([codon[2] for codon in codons]).issuperset(set(meanings))]
+ set2 = set([codon[1] for codon in codons])
+ set3 = set([codon[2] for codon in codons])
+ candidates = set([c1+c2+c3 for c1 in c1_list for c2 in c2_list for c3 in c3_list])
+ candidates.difference_update(codons)
+ answer = codons[:] #copy
+ #print "Have %i new candidates" % len(candidates)
+ for ambig_codon in candidates :
+ wanted = True
+ #e.g. 'TRR' -> 'TAA', 'TAG', 'TGA', 'TGG'
+ for codon in [c1+c2+c3 \
+ for c1 in ambiguous_nucleotide_values[ambig_codon[0]] \
+ for c2 in ambiguous_nucleotide_values[ambig_codon[1]] \
+ for c3 in ambiguous_nucleotide_values[ambig_codon[2]]]:
+ if codon not in codons :
+ #This ambiguous codon can code for a non-stop, exclude it!
+ wanted=False
+ #print "Rejecting %s" % ambig_codon
+ continue
+ if wanted :
+ answer.append(ambig_codon)
+ return answer
+assert list_ambiguous_codons(['TGA', 'TAA'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TRA']
+assert list_ambiguous_codons(['TAG', 'TGA'],IUPACData.ambiguous_dna_values) == ['TAG', 'TGA']
+assert list_ambiguous_codons(['TAG', 'TAA'],IUPACData.ambiguous_dna_values) == ['TAG', 'TAA', 'TAR']
+assert list_ambiguous_codons(['UAG', 'UAA'],IUPACData.ambiguous_rna_values) == ['UAG', 'UAA', 'UAR']
+assert list_ambiguous_codons(['TGA', 'TAA', 'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']
+
+# Forward translation is "onto", that is, any given codon always maps
+# to the same protein, or it doesn't map at all. Thus, I can build
+# off of an existing table to produce the ambiguous mappings.
+#
+# This handles the general case. Perhaps it's overkill?
+# >>> t = CodonTable.ambiguous_dna_by_id[1]
+# >>> t.forward_table["AAT"]
+# 'N'
+# >>> t.forward_table["GAT"]
+# 'D'
+# >>> t.forward_table["RAT"]
+# 'B'
+# >>> t.forward_table["YTA"]
+# 'L'
+
+class AmbiguousForwardTable:
+ def __init__(self, forward_table, ambiguous_nucleotide, ambiguous_protein):
+ self.forward_table = forward_table
+
+ self.ambiguous_nucleotide = ambiguous_nucleotide
+ self.ambiguous_protein = ambiguous_protein
+
+ inverted = {}
+ for name, val in ambiguous_protein.items():
+ for c in val:
+ x = inverted.get(c, {})
+ x[name] = 1
+ inverted[c] = x
+ for name, val in inverted.items():
+ inverted[name] = val.keys()
+ self._inverted = inverted
+
+ self._cache = {}
+
+ def get(self, codon, failobj = None):
+ try:
+ return self.__getitem__(codon)
+ except KeyError:
+ return failobj
+
+ def __getitem__(self, codon):
+ try:
+ x = self._cache[codon]
+ except KeyError:
+ pass
+ else:
+ if x is TranslationError:
+ raise TranslationError(codon) # no unique translation
+ if x is KeyError:
+ raise KeyError(codon) # it's a stop codon
+ return x
+ try:
+ x = self.forward_table[codon]
+ self._cache[codon] = x
+ return x
+ except KeyError:
+ pass
+
+ # XXX Need to make part of this into a method which returns
+ # a list of all possible encodings for a codon!
+ try:
+ possible = list_possible_proteins(codon,
+ self.forward_table,
+ self.ambiguous_nucleotide)
+ except KeyError:
+ self._cache[codon] = KeyError
+ raise KeyError(codon) # stop codon
+ except TranslationError:
+ self._cache[codon] = TranslationError
+ raise TranslationError(codon) # does not code
+ assert len(possible) > 0, "unambiguous codons must code"
+
+ # Hah! Only one possible protein, so use it
+ if len(possible) == 1:
+ self._cache[codon] = possible[0]
+ return possible[0]
+
+ # See if there's an ambiguous protein encoding for the multiples.
+ # Find residues which exist in every coding set.
+ ambiguous_possible = {}
+ for amino in possible:
+ for term in self._inverted[amino]:
+ ambiguous_possible[term] = ambiguous_possible.get(term, 0) + 1
+
+ n = len(possible)
+ possible = []
+ for amino, val in ambiguous_possible.items():
+ if val == n:
+ possible.append(amino)
+
+ # No amino acid encoding for the results
+ if len(possible) == 0:
+ self._cache[codon] = TranslationError
+ raise TranslationError(codon) # no valid translation
+
+ # All of these are valid, so choose one
+ # To be unique, sort by smallet ambiguity then alphabetically
+ # Can get this if "X" encodes for everything.
+ def _sort(x, y, table = self.ambiguous_protein):
+ a = cmp(len(table[x]), len(table[y]))
+ if a == 0:
+ return cmp(x, y)
+ return a
+ possible.sort(_sort)
+
+ x = possible[0]
+ self._cache[codon] = x
+ return x
+
+#Prepare the ambiguous tables for DNA, RNA and Generic (DNA or RNA)
+ambiguous_dna_by_name = {}
+for key, val in unambiguous_dna_by_name.items():
+ ambiguous_dna_by_name[key] = AmbiguousCodonTable(val,
+ IUPAC.ambiguous_dna,
+ IUPACData.ambiguous_dna_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+ambiguous_dna_by_id = {}
+for key, val in unambiguous_dna_by_id.items():
+ ambiguous_dna_by_id[key] = AmbiguousCodonTable(val,
+ IUPAC.ambiguous_dna,
+ IUPACData.ambiguous_dna_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+
+ambiguous_rna_by_name = {}
+for key, val in unambiguous_rna_by_name.items():
+ ambiguous_rna_by_name[key] = AmbiguousCodonTable(val,
+ IUPAC.ambiguous_rna,
+ IUPACData.ambiguous_rna_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+ambiguous_rna_by_id = {}
+for key, val in unambiguous_rna_by_id.items():
+ ambiguous_rna_by_id[key] = AmbiguousCodonTable(val,
+ IUPAC.ambiguous_rna,
+ IUPACData.ambiguous_rna_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+
+#The following isn't very elegant, but seems to work nicely.
+_merged_values = dict(IUPACData.ambiguous_rna_values.iteritems())
+_merged_values["T"] = "U"
+
+for key, val in generic_by_name.items():
+ ambiguous_generic_by_name[key] = AmbiguousCodonTable(val,
+ Alphabet.NucleotideAlphabet(),
+ _merged_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+
+for key, val in generic_by_id.items():
+ ambiguous_generic_by_id[key] = AmbiguousCodonTable(val,
+ Alphabet.NucleotideAlphabet(),
+ _merged_values,
+ IUPAC.extended_protein,
+ IUPACData.extended_protein_values)
+del _merged_values
+del key, val
+
+#Basic sanity test,
+for n in ambiguous_generic_by_id.keys() :
+ assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V"
+ assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V"
+ assert ambiguous_rna_by_id[n].forward_table["UUN"] == "X" #F or L
+ #R = A or G, so URR = UAA or UGA / TRA = TAA or TGA = stop codons
+ if "UAA" in unambiguous_rna_by_id[n].stop_codons \
+ and "UGA" in unambiguous_rna_by_id[n].stop_codons :
+ try :
+ print ambiguous_dna_by_id[n].forward_table["TRA"]
+ assert False, "Should be a stop only"
+ except KeyError :
+ pass
+ assert "URA" in ambiguous_generic_by_id[n].stop_codons
+ assert "URA" in ambiguous_rna_by_id[n].stop_codons
+ assert "TRA" in ambiguous_generic_by_id[n].stop_codons
+ assert "TRA" in ambiguous_dna_by_id[n].stop_codons
+del n
+assert ambiguous_generic_by_id[1].stop_codons == ambiguous_generic_by_name["Standard"].stop_codons
+assert ambiguous_generic_by_id[4].stop_codons == ambiguous_generic_by_name["SGC3"].stop_codons
+assert ambiguous_generic_by_id[15].stop_codons == ambiguous_generic_by_name['Blepharisma Macronuclear'].stop_codons
--- /dev/null
+# Information about the IUPAC alphabets
+
+protein_letters = "ACDEFGHIKLMNPQRSTVWY"
+extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO"
+# B = "Asx"; aspartic acid or asparagine (D or N)
+# X = "Xxx"; unknown or 'other' amino acid
+# Z = "Glx"; glutamic acid or glutamine (E or Q)
+# J = "Xle"; leucine or isoleucine (L or I, used in mass-spec)
+# U = "Sec"; selenocysteine
+# O = "Pyl"; pyrrolysine
+ambiguous_dna_letters = "GATCRYWSMKHBVDN"
+unambiguous_dna_letters = "GATC"
+ambiguous_rna_letters = "GAUCRYWSMKHBVDN"
+unambiguous_rna_letters = "GAUC"
+
+# B == 5-bromouridine
+# D == 5,6-dihydrouridine
+# S == thiouridine
+# W == wyosine
+extended_dna_letters = "GATCBDSW"
+
+# are there extended forms?
+#extended_rna_letters = "GAUCBDSW"
+
+ambiguous_dna_values = {
+ "A": "A",
+ "C": "C",
+ "G": "G",
+ "T": "T",
+ "M": "AC",
+ "R": "AG",
+ "W": "AT",
+ "S": "CG",
+ "Y": "CT",
+ "K": "GT",
+ "V": "ACG",
+ "H": "ACT",
+ "D": "AGT",
+ "B": "CGT",
+ "X": "GATC",
+ "N": "GATC",
+ }
+ambiguous_rna_values = {
+ "A": "A",
+ "C": "C",
+ "G": "G",
+ "U": "U",
+ "M": "AC",
+ "R": "AG",
+ "W": "AU",
+ "S": "CG",
+ "Y": "CU",
+ "K": "GU",
+ "V": "ACG",
+ "H": "ACU",
+ "D": "AGU",
+ "B": "CGU",
+ "X": "GAUC",
+ "N": "GAUC",
+ }
+
+ambiguous_dna_complement = {
+ "A": "T",
+ "C": "G",
+ "G": "C",
+ "T": "A",
+ "M": "K",
+ "R": "Y",
+ "W": "W",
+ "S": "S",
+ "Y": "R",
+ "K": "M",
+ "V": "B",
+ "H": "D",
+ "D": "H",
+ "B": "V",
+ "X": "X",
+ "N": "N",
+ }
+
+ambiguous_rna_complement = {
+ "A": "U",
+ "C": "G",
+ "G": "C",
+ "U": "A",
+ "M": "K",
+ "R": "Y",
+ "W": "W",
+ "S": "S",
+ "Y": "R",
+ "K": "M",
+ "V": "B",
+ "H": "D",
+ "D": "H",
+ "B": "V",
+ "X": "X",
+ "N": "N",
+ }
+
+
+def _make_ranges(dict):
+ d = {}
+ for key, value in dict.items():
+ d[key] = (value, value)
+ return d
+
+# From bioperl's SeqStats.pm
+unambiguous_dna_weights = {
+ "A": 347.,
+ "C": 323.,
+ "G": 363.,
+ "T": 322.,
+ }
+unambiguous_dna_weight_ranges = _make_ranges(unambiguous_dna_weights)
+
+unambiguous_rna_weights = {
+ "A": unambiguous_dna_weights["A"] + 16., # 16 for the oxygen
+ "C": unambiguous_dna_weights["C"] + 16.,
+ "G": unambiguous_dna_weights["G"] + 16.,
+ "U": 340.,
+}
+unambiguous_rna_weight_ranges = _make_ranges(unambiguous_rna_weights)
+
+def _make_ambiguous_ranges(dict, weight_table):
+ range_d = {}
+ avg_d = {}
+ for letter, values in dict.items():
+ #Following line is a quick hack to skip undefined weights for U and O
+ if len(values)==1 and values[0] not in weight_table : continue
+ weights = map(weight_table.get, values)
+ range_d[letter] = (min(weights), max(weights))
+ total_w = 0.0
+ for w in weights:
+ total_w = total_w + w
+ avg_d[letter] = total_w / len(weights)
+ return range_d, avg_d
+
+ambiguous_dna_weight_ranges, avg_ambiguous_dna_weights = \
+ _make_ambiguous_ranges(ambiguous_dna_values,
+ unambiguous_dna_weights)
+
+ambiguous_rna_weight_ranges, avg_ambiguous_rna_weights = \
+ _make_ambiguous_ranges(ambiguous_rna_values,
+ unambiguous_rna_weights)
+
+protein_weights = {
+ "A": 89.09,
+ "C": 121.16,
+ "D": 133.10,
+ "E": 147.13,
+ "F": 165.19,
+ "G": 75.07,
+ "H": 155.16,
+ "I": 131.18,
+ "K": 146.19,
+ "L": 131.18,
+ "M": 149.21,
+ "N": 132.12,
+ #"O": 0.0, # Needs to be recorded!
+ "P": 115.13,
+ "Q": 146.15,
+ "R": 174.20,
+ "S": 105.09,
+ "T": 119.12,
+ #"U": 168.05, # To be confirmed
+ "V": 117.15,
+ "W": 204.23,
+ "Y": 181.19
+ }
+
+extended_protein_values = {
+ "A": "A",
+ "B": "ND",
+ "C": "C",
+ "D": "D",
+ "E": "E",
+ "F": "F",
+ "G": "G",
+ "H": "H",
+ "I": "I",
+ "J": "IL",
+ "K": "K",
+ "L": "L",
+ "M": "M",
+ "N": "N",
+ "O": "O",
+ "P": "P",
+ "Q": "Q",
+ "R": "R",
+ "S": "S",
+ "T": "T",
+ "U": "U",
+ "V": "V",
+ "W": "W",
+ "X": "ACDEFGHIKLMNPQRSTVWY",
+ #TODO - Include U and O in the possible values of X?
+ #This could alter the extended_protein_weight_ranges ...
+ "Y": "Y",
+ "Z": "QE",
+}
+
+protein_weight_ranges = _make_ranges(protein_weights)
+
+extended_protein_weight_ranges, avg_extended_protein_weights = \
+ _make_ambiguous_ranges(extended_protein_values,
+ protein_weights)
+
+
+
--- /dev/null
+# This is a Python module
+"""Collections of various bits of useful biological data.
+"""
--- /dev/null
+# Copyright 2002 by Andrew Dalke.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+"""Decode elements from a Std/Martel parsed XML stream (OBSOLETE).
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+(and therefore Bio.Decode) have been deprecated. They are no longer used in
+any of the current Biopython parsers, and are likely to be removed in a
+future release."""
+
+import warnings
+warnings.warn("Martel and those parts of Biopython depending on it" \
+ +" directly (such as Bio.Mindy and Bio.Decode) are now" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+
+import string
+from Bio.Parsers.spark import GenericScanner, GenericParser
+
+def unescape_C(s):
+ result = []
+ for i in range(len(s)):
+ if s[i] != "\\":
+ result.append(s[i])
+ continue
+ c = s[i+1:i+2]
+ if c == "x":
+ x = s[i+2:i+4]
+ if len(x) != 2:
+ raise ValueError("invalid \\x escape")
+ i = int(x, 16)
+ result.append(chr(i))
+ continue
+ if c in "01234567":
+ x = s[i+1:i+4]
+ # \octals don't do a length assertion check
+ i = int(x, 8)
+ result.append(chr(i))
+ continue
+ result.append(c)
+ return "".join(result)
+
+def join_english(fields):
+ if not fields:
+ return ""
+ s = fields[0]
+ for field in fields[1:]:
+ if s[-1:] == "-" and s[-3:-2] == "-":
+ s = s + field
+ continue
+ if s.find(" ") == -1 and field.find(" ") == -1:
+ s = s + field
+ continue
+ s = s + " " + field
+ return (" ".join(s.split())).strip()
+
+
+
+def chomp(s, c):
+ if s[-1:] == c:
+ return s[:-1]
+ return s
+
+def lchomp(s, c):
+ if s[:1] == c:
+ return s[1:]
+ return s
+
+def chompchomp(s, c):
+ if s[:1] == c and s[-1:] == c:
+ return s[1:-1]
+ return s
+
+def fixspaces(s):
+ # s.split breaks down to a list of words
+ # " ".join puts them together
+ # strip removes leading and trailing spaces
+ return " ".join(s.split()).strip()
+
+def join_fixspaces(lines):
+ return " ".join((" ".join(lines)).split()).strip()
+
+def tr(s, frm, to):
+ table = string.maketrans(frm, to)
+ return s.translate(table)
+
+def safe_int(s):
+ """converts to int if the number is small, long if it's large"""
+ try:
+ return int(s)
+ except ValueError:
+ return long(s)
+
+decode_functions = {
+ "chomp": (chomp, str, str),
+ "chompchomp": (chompchomp, str, str),
+ "chop": (lambda s: s[:-1], str, str),
+ "chopchop": (lambda s: s[1:-1], str, str),
+ "fixspaces": (fixspaces, str, str),
+ "lchomp": (lchomp, str, str),
+ "lchop": (lambda s: s[1:], str, str),
+ "lower": (lambda s: s.lower(), str, str),
+ "lstrip": (lambda s: s.lstrip(), str, str),
+ "replace": (lambda s, old, new: s.replace(old, new), str, str),
+ "rstrip": (lambda s: s.rstrip(), str, str),
+ "str": (str, str, str),
+ "strip": (lambda s: s.strip(), str, str),
+ "tr": (tr, str, str),
+ "unescape.c": (unescape_C, str, str),
+ "unescape.doublequote": (lambda s: s.replace('""', '"'), str, str),
+ "unescape.singlequote": (lambda s: s.replace("''", "'"), str, str),
+ "upper": (lambda s: s.upper(), str, str),
+
+ # List operations
+ "join": (lambda lst, s = " ": s.join(lst), list, str),
+ "join.english": (join_english, list, str),
+
+ # Integer operations
+ "int": (safe_int, [float, str, int], int),
+ "int.comma": (lambda s: safe_int(s.replace(",", "")),
+ [float, str, int], int),
+ "hex": (hex, str, int),
+ "oct": (oct, str, int),
+ "add": ((lambda i, j: i+j), int, int),
+
+ # Float operations
+ "float": (float, (float, str, int), float),
+
+ }
+
+def _fixup_defs():
+ # Normalize so the 2nd and 3rd terms are tuples
+ for k, v in decode_functions.items():
+ f, in_types, out_types = v
+ if isinstance(in_types, type([])):
+ in_types = tuple(in_types)
+ elif not isinstance(in_types, type( () )):
+ in_types = (in_types,)
+
+ if isinstance(out_types, type([])):
+ out_types = tuple(out_types)
+ elif not isinstance(out_types, type( () )):
+ out_types = (out_types,)
+
+ decode_functions[k] = (f, in_types, out_types)
+_fixup_defs()
+
+class Token:
+ def __init__(self, type):
+ self.type = type
+ def __cmp__(self, other):
+ return cmp(self.type, other)
+ def __repr__(self):
+ return "Token(%r)" % (self.type,)
+
+class ValueToken(Token):
+ def __init__(self, type, val):
+ Token.__init__(self, type)
+ self.val = val
+ def __cmp__(self, other):
+ return cmp(self.type, other)
+ def __repr__(self):
+ return "%s(%r)" % (self.__class__.__name__, self.val)
+ def __str__(self):
+ return str(self.val)
+
+class Integer(ValueToken):
+ def __init__(self, val):
+ ValueToken.__init__(self, "integer", val)
+
+class Float(ValueToken):
+ def __init__(self, val):
+ ValueToken.__init__(self, "float", val)
+
+class String(ValueToken):
+ def __init__(self, val):
+ ValueToken.__init__(self, "string", val)
+
+class FunctionName(ValueToken):
+ def __init__(self, val):
+ ValueToken.__init__(self, "functionname", val)
+
+class DecodeScanner(GenericScanner):
+ def __init__(self):
+ GenericScanner.__init__(self)
+
+ def tokenize(self, input):
+ self.rv = []
+ GenericScanner.tokenize(self, input)
+ return self.rv
+
+ def t_functionname(self, input):
+ r" \w+(\.\w+)*"
+ self.rv.append(FunctionName(input))
+
+ def t_pipe(self, input):
+ r" \| "
+ self.rv.append(Token("pipe"))
+
+ def t_open_paren(self, input):
+ r" \( "
+ self.rv.append(Token("open_paren"))
+
+ def t_close_paren(self, input):
+ r" \) "
+ self.rv.append(Token("close_paren"))
+
+ def t_comma(self, input):
+ r" , "
+ self.rv.append(Token("comma"))
+
+ def t_whitespace(self, input):
+ r" \s+ "
+ pass
+
+ def t_string(self, input):
+ r""" "([^"\\]+|\\.)*"|'([^'\\]+|\\.)*' """
+ # "' # emacs cruft
+ s = input[1:-1]
+ s = unescape_C(s)
+
+ self.rv.append(String(s))
+
+ def t_float(self, input):
+ r""" [+-]?((\d+(\.\d*)?)|\.\d+)([eE][+-]?[0-9]+)? """
+ # See if this is an integer
+ try:
+ self.rv.append(Integer(safe_int(input)))
+ except ValueError:
+ self.rv.append(Float(float(input)))
+
+class Function:
+ def __init__(self, name, args = ()):
+ self.name = name
+ self.args = args
+ def __str__(self):
+ args = self.args
+ if not args:
+ s = ""
+ else:
+ s = str(args)[1:-1]
+ return "%s(x, %s)" % (self.name, s)
+ __repr__ = __str__
+
+class DecodeParser(GenericParser):
+ def __init__(self, start = "expression"):
+ GenericParser.__init__(self, start)
+ self.begin_pos = 0
+
+ def p_expression(self, args):
+ """
+ expression ::= term
+ expression ::= term pipe expression
+ """
+ if len(args) == 1:
+ return [args[0]]
+ return [args[0]] + args[2]
+
+ def p_term(self, args):
+ """
+ term ::= functionname
+ term ::= functionname open_paren args close_paren
+ """
+ if len(args) == 1:
+ return Function(args[0].val)
+ return Function(args[0].val, tuple([x.val for x in args[2]]))
+
+ def p_args(self, args):
+ """
+ args ::= arg
+ args ::= arg comma args
+ """
+ if len(args) == 1:
+ return [args[0]]
+ return [args[0]] + args[2]
+
+ def p_arg(self, args):
+ """
+ arg ::= string
+ arg ::= integer
+ arg ::= float
+ """
+ return args[0]
+
+def scan(input):
+ scanner = DecodeScanner()
+ return scanner.tokenize(input)
+
+def parse(tokens):
+ parser = DecodeParser()
+ return parser.parse(tokens)
+
+_decoder_cache = {}
+
+class FunctionCall:
+ def __init__(self, f, args):
+ self.f = f
+ self.args = args
+ def __call__(self, x):
+ return self.f(x, *self.args)
+
+class FunctionCallChain:
+ def __init__(self, inner_f, f, args):
+ self.inner_f = inner_f
+ self.f = f
+ self.args = args
+ def __call__(self, x):
+ return self.f(self.inner_f(x), *self.args)
+
+#### I don't think this is the right way to do things
+##class CheckTypes:
+## def __init__(self, f, call_types, return_types):
+## self.f = f
+## self.call_types = call_types
+## self.return_types = return_types
+## def __call__(self, x):
+## if self.call_types is not None:
+## for T in self.call_types:
+## if isinstance(x, T):
+## break
+## else:
+## raise TypeError(
+## "Call value %s of type %s, expecting one of %s" %
+## (x, type(x).__name__,
+## [T.name for T in self.call_types]))
+## y = self.f(x)
+
+## if not self.return_types:
+## return y
+
+## for T in self.return_types:
+## if isinstance(y, T):
+## return y
+## raise TypeError("Return value %s of type %s, expecting one of %s" %
+## (y, type(y).__name__,
+## [T.name for T in self.return_types]))
+
+def make_decoder(s):
+ try:
+ return _decoder_cache[s]
+ except KeyError:
+ pass
+
+ functions = parse(scan(s))
+
+ f = functions[0]
+ fc = decode_functions[f.name][0]
+ args = f.args
+ if args:
+ fc = FunctionCall(fc, args)
+ for f in functions[1:]:
+ fc = FunctionCallChain(fc, decode_functions[f.name][0], f.args)
+ _decoder_cache[s] = fc
+ return fc
+
+def _verify_subtypes(subset, total, old_name, new_name):
+ for x in subset:
+ if x not in total:
+ raise TypeError("%s can produce a %r value not accepted by %s" %
+ (old_name, x.__name__, new_name))
+
+_typechecked_decoder_cache = {}
+def make_typechecked_decoder(s, input_types = None, output_types = None):
+ cache_lookup = (s, input_types, output_types)
+ try:
+ return _typechecked_decoder_cache[cache_lookup]
+ except KeyError:
+ pass
+ if input_types is not None and not isinstance(input_types, type( () )):
+ input_types = (input_types,)
+ if output_types is not None and not isinstance(output_types, type( () )):
+ output_types = (output_types,)
+
+ functions = parse(scan(s))
+
+ # Make sure the input type(s) are allowed
+ f = functions[0]
+ fc, in_types, out_types = decode_functions[f.name]
+ if input_types is not None:
+ for x in input_types:
+ if x not in in_types:
+ raise TypeError(
+ "the input type includes %r which isn't supported by %s" %
+ (x.__name__, f.name))
+
+ # Do the composition
+ old_name = f.name
+ input_types = out_types
+ args = functions[0].args
+ if args:
+ fc = FunctionCall(fc, args)
+
+ for f in functions[1:]:
+ transform_func, in_types, out_types = decode_functions[f.name]
+ _verify_subtypes(input_types, in_types, old_name, f.name)
+ old_name = f.name
+ input_types = out_types
+ fc = FunctionCallChain(fc, transform_func, f.args)
+
+ if output_types is not None:
+ _verify_subtypes(input_types, output_types, old_name, "the output")
+ _typechecked_decoder_cache[cache_lookup] = fc
+ return fc
+
+
+def test():
+ assert make_decoder("chop")("Andrew") == "Andre"
+ assert make_decoder("int")("9") == 9
+ assert make_decoder('join(" ")')(["Andrew", "Dalke"]) == \
+ "Andrew Dalke"
+ assert make_decoder('chomp("|")')("|test|") == "|test"
+ assert make_decoder('chomp("|")')("|test") == "|test"
+ assert make_decoder('chomp("A")|chop')("BA") == ""
+ assert make_decoder('chomp("A")|chop')("AB") == "A"
+ assert make_decoder('chop|chomp("A")')("AB") == ""
+ assert make_decoder('chop|chomp("A")')("BA") == "B"
+ assert make_decoder('add(5)')(2) == 7
+ assert make_decoder('add(-2)')(5) == 3
+
+if __name__ == "__main__":
+ test()
--- /dev/null
+#!/usr/bin/env python
+#
+# Copyright 2002-2003 by Michael Hoffman. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""
+Bio.DocSQL: easy access to DB API databases.
+
+>>> import DocSQL, MySQLdb, os
+>>> db=MySQLdb.connect(passwd='', db='test')
+>>> class CreatePeople(DocSQL.Create):
+... \"""
+... CREATE TEMPORARY TABLE people
+... (id INT UNSIGNED NOT NULL PRIMARY KEY AUTO_INCREMENT,
+... last_name TINYTEXT,
+... first_name TINYTEXT)
+... \"""
+...
+>>> CreatePeople(connection=db)
+CreatePeople(message=Success)
+"""
+
+__version__ = "$Revision: 1.13 $"
+# $Source: /home/repository/biopython/biopython/Bio/DocSQL.py,v $
+
+import exceptions
+import sys
+
+from Bio import MissingExternalDependencyError
+
+try:
+ import MySQLdb
+except:
+ raise MissingExternalDependencyError("Install MySQLdb if you want to use Bio.DocSQL.")
+
+connection = None
+
+class NoInsertionError(exceptions.Exception):
+ pass
+
+def _check_is_public(name):
+ if name[:6] == "_names":
+ raise AttributeError
+
+class QueryRow(list):
+ def __init__(self, cursor):
+ try:
+ row = cursor.fetchone()
+ super(QueryRow, self).__init__(row)
+ except TypeError:
+ raise StopIteration
+
+ object.__setattr__(self, "_names", [x[0] for x in cursor.description]) # FIXME: legacy
+ object.__setattr__(self, "_names_hash", {})
+
+ for i, name in enumerate(self._names):
+ self._names_hash[name] = i
+
+ def __getattr__(self, name):
+ _check_is_public(name)
+ try:
+ return self[self._names_hash[name]]
+ except (KeyError, AttributeError) :
+ raise AttributeError("'%s' object has no attribute '%s'" \
+ % (self.__class__.__name__, name))
+
+ def __setattr__(self, name, value):
+ try:
+ self._names_hash
+ except AttributeError:
+ return object.__setattr__(self, name, value)
+
+ _check_is_public(name)
+ try:
+ index = self._names_hash[name]
+ self[index] = value
+ except KeyError:
+ return object.__setattr__(self, name, value)
+
+class Query(object):
+ """
+ SHOW TABLES
+ """
+ MSG_FAILURE = "Failure"
+ MSG_SUCCESS = "Success"
+ message = "not executed"
+ error_message = ""
+ prefix = ""
+ suffix = ""
+ row_class = QueryRow
+
+ def __init__(self, *args, **keywds):
+ try:
+ self.connection = keywds['connection']
+ except KeyError:
+ self.connection = connection
+ try:
+ self.diagnostics = keywds['diagnostics']
+ except KeyError:
+ self.diagnostics = 0
+
+ self.statement = self.prefix + self.__doc__ + self.suffix
+ self.params = args
+
+ def __iter__(self):
+ return IterationCursor(self, self.connection)
+
+ def __repr__(self):
+ return "%s(message=%s)" % (self.__class__.__name__, self.message)
+
+ def cursor(self):
+ return iter(self).cursor
+
+ def dump(self):
+ for item in self:
+ print item
+
+class QueryGeneric(Query):
+ def __init__(self, statement, *args, **keywds):
+ Query.__init__(self, *args, **keywds)
+ self.statement = statement,
+
+class IterationCursor(object):
+ def __init__(self, query, connection=connection):
+ if connection is None:
+ raise TypeError("database connection is None")
+ self.cursor = connection.cursor()
+ self.row_class = query.row_class
+ if query.diagnostics:
+ print >>sys.stderr, query.statement
+ print >>sys.stderr, query.params
+ self.cursor.execute(query.statement, query.params)
+
+ def next(self):
+ return self.row_class(self.cursor)
+
+class QuerySingle(Query, QueryRow):
+ ignore_warnings = 0
+ def __init__(self, *args, **keywds):
+ message = self.MSG_FAILURE
+ Query.__init__(self, *args, **keywds)
+ try:
+ self.single_cursor = Query.cursor(self)
+ except MySQLdb.Warning:
+ if not self.ignore_warnings:
+ raise
+ self.row_class.__init__(self, self.cursor())
+ object.__setattr__(self, "message", self.MSG_SUCCESS)
+
+ def cursor(self):
+ return self.single_cursor
+
+class QueryAll(list, Query):
+ def __init__(self, *args, **keywds):
+ Query.__init__(self, *args, **keywds)
+ list.__init__(self, map(self.process_row, self.cursor().fetchall()))
+
+ def process_row(self, row):
+ return row
+
+class QueryAllFirstItem(QueryAll):
+ def process_row(self, row):
+ return row[0]
+
+class Create(QuerySingle):
+ def __init__(self, *args, **keywds):
+ try:
+ QuerySingle.__init__(self, *args, **keywds)
+ except StopIteration:
+ self.message = self.MSG_SUCCESS
+
+class Update(Create):
+ pass
+
+class Insert(Create):
+ MSG_INTEGRITY_ERROR = "Couldn't insert: %s. "
+
+ def __init__(self, *args, **keywds):
+ try:
+ Create.__init__(self, *args, **keywds)
+ except MySQLdb.IntegrityError, error_data:
+ self.error_message += self.MSG_INTEGRITY_ERROR % error_data[1]
+ try:
+ self.total_count
+ except AttributeError:
+ self.total_count = 0
+
+ raise MySQLdb.IntegrityError(self.error_message)
+
+ self.id = self.cursor().insert_id()
+ try:
+ self.total_count += self.cursor().rowcount
+ except AttributeError:
+ self.total_count = self.cursor().rowcount
+
+ if self.cursor().rowcount == 0:
+ raise NoInsertionError
+
+def _test(*args, **keywds):
+ import doctest, sys
+ doctest.testmod(sys.modules[__name__], *args, **keywds)
+
+if __name__ == "__main__":
+ if __debug__:
+ _test()
--- /dev/null
+# Set up the IUPAC alphabet properties
+
+
+from Bio.PropertyManager import default_manager
+from Bio import Alphabet
+from Bio.Alphabet import IUPAC
+from Bio.Data import IUPACData
+
+from Bio import Transcribe, Translate
+
+set_prop = default_manager.class_property
+
+# weight tables
+set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
+ IUPACData.unambiguous_dna_weights
+set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
+ IUPACData.avg_ambiguous_dna_weights
+set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
+ IUPACData.unambiguous_rna_weights
+set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
+ IUPACData.avg_ambiguous_rna_weights
+set_prop[IUPAC.IUPACProtein]["weight_table"] = \
+ IUPACData.protein_weights
+set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
+ IUPACData.avg_extended_protein_weights
+
+set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
+ IUPACData.unambiguous_dna_weight_ranges
+set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
+ IUPACData.ambiguous_dna_weight_ranges
+set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
+ IUPACData.unambiguous_rna_weight_ranges
+set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
+ IUPACData.ambiguous_rna_weight_ranges
+set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
+ IUPACData.protein_weight_ranges
+set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
+ IUPACData.extended_protein_weight_ranges
+
+
+
+# transcriber objects
+
+set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
+ Transcribe.generic_transcriber
+
+set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
+ Transcribe.ambiguous_transcriber
+
+set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
+ Transcribe.unambiguous_transcriber
+
+
+set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
+ Transcribe.generic_transcriber
+
+set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
+ Transcribe.ambiguous_transcriber
+
+set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
+ Transcribe.unambiguous_transcriber
+
+
+# translator objects
+for name, obj in Translate.unambiguous_dna_by_name.items():
+ property = "translator.name." + name
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+for name, obj in Translate.unambiguous_rna_by_name.items():
+ property = "translator.name." + name
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "rna_translator.name." + name
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+
+for id, obj in Translate.unambiguous_dna_by_id.items():
+ property = "translator.id.%d" % id
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+ if id == 1:
+ set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+ set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
+
+
+for id, obj in Translate.unambiguous_rna_by_id.items():
+ property = "translator.id.%d" % id
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "rna_translator.id.%d" % id
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+ if id == 1:
+ set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+ set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
+
+# ambiguous translator objects
+for name, obj in Translate.ambiguous_dna_by_name.items():
+ property = "translator.name." + name
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "ambiguous_translator.name." + name
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+for name, obj in Translate.ambiguous_rna_by_name.items():
+ property = "translator.name." + name
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "ambiguous_rna_translator.name." + name
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+
+for id, obj in Translate.ambiguous_dna_by_id.items():
+ property = "translator.id.%d" % id
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "ambiguous_translator.id.%d" % id
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+ if id == 1:
+ set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+ set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
+
+
+for id, obj in Translate.ambiguous_rna_by_id.items():
+ property = "translator.id.%d" % id
+ set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+ property = "ambiguous_rna_translator.id.%d" % id
+ set_prop[obj.table.protein_alphabet.__class__][property] = obj
+ if id == 1:
+ set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+ set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj
--- /dev/null
+# This is a Python module.
+"""Properties for functionality such as transcription and translation.
+"""
--- /dev/null
+"""
+Code to deal with alignments written in Fasta format (OBSOLETE).
+
+This module is considered obsolete and likely to be deprecated. Please use
+Bio.AlignIO instead for reading and writing alignments in FASTA format.
+
+This mostly just uses the regular Fasta parsing stuff written by Jeff
+to deal with all of the input and output formats.
+
+functions:
+o parse_file()
+
+classes:
+FastaAlignment"""
+# standard library
+import os
+
+# biopython
+from Bio.Align.Generic import Alignment
+from Bio import Alphabet
+from Bio.Alphabet import IUPAC
+from Bio import Fasta
+
+def parse_file(file_name, type = 'DNA'):
+ """Parse the given file into a FastaAlignment object.
+
+ Arguments:
+ o file_name - The location of the file to parse.
+ o type - The type of information contained in the file.
+ """
+ if type.upper() == 'DNA':
+ alphabet = IUPAC.ambiguous_dna
+ elif type.upper() == 'RNA':
+ alphabet = IUPAC.ambiguous_rna
+ elif type.upper() == 'PROTEIN':
+ alphabet = IUPAC.protein
+ else:
+ raise ValueError("Invalid type %s passed. Need DNA, RNA or PROTEIN"
+ % type)
+
+ # create a new alignment object
+ fasta_align = FastaAlignment(Alphabet.Gapped(alphabet))
+
+ # now parse the file and fill up the alignment object
+ align_file = open(file_name, 'r')
+
+ parser = Fasta.RecordParser()
+ iterator = Fasta.Iterator(align_file, parser)
+
+ cur_align = iterator.next()
+ while cur_align:
+ fasta_align.add_sequence(cur_align.title, cur_align.sequence)
+
+ cur_align = iterator.next()
+
+ return fasta_align
+
+class FastaAlignment(Alignment):
+ """Work with the Fasta Alignment format.
+
+ The fasta alignment format is basically the same as the regular ol'
+ Fasta format we know and love, except the sequences have gaps
+ (represented by -'s).
+ """
+ def __init__(self, alphabet = Alphabet.Gapped(IUPAC.ambiguous_dna)):
+ Alignment.__init__(self, alphabet)
+
+ def __str__(self):
+ """Print out a fasta version of the alignment info."""
+ return_string = ''
+ for item in self._records:
+ new_f_record = Fasta.Record()
+ new_f_record.title = item.description
+ new_f_record.sequence = item.seq.data
+
+ return_string = return_string + str(new_f_record) + os.linesep + os.linesep
+
+ # have a extra newline, so strip two off and add one before returning
+ return return_string.rstrip() + os.linesep
+
+
+
+
+
--- /dev/null
+"""Utilities for working with FASTA-formatted sequences (OBSOLETE).
+
+Classes:
+Record Holds FASTA sequence data.
+Iterator Iterates over sequence data in a FASTA file.
+RecordParser Parses FASTA sequence data into a Record object.
+SequenceParser Parses FASTA sequence data into a SeqRecord object.
+
+For a long time this module was the most commonly used and best documented
+FASTA parser in Biopython. However, we now recommend using Bio.SeqIO instead.
+
+In view of this, while you can continue to use Bio.Fasta for the moment, it is
+considered to be a legacy module and should not be used if you are writing new
+code. At some point Bio.Fasta may be officially deprecated (with warning
+messages when used) before finally being removed.
+
+If you are already using Bio.Fasta with the SequenceParser to get SeqRecord
+objects, then you should be able to switch to the more recent Bio.SeqIO module
+very easily as that too uses SeqRecord objects. For example,
+
+from Bio import Fasta
+handle = open("example.fas")
+for seq_record in Fasta.Iterator(handle, Fasta.SequenceParser()) :
+ print seq_record.description
+ print seq_record.seq
+handle.close()
+
+Using Bio.SeqIO instead this becomes:
+
+from Bio import SeqIO
+handle = open("example.fas")
+for seq_record in SeqIO.parse(handle, "fasta") :
+ print seq_record.description
+ print seq_record.seq
+handle.close()
+
+Converting an existing code which uses the RecordParser is a little more
+complicated as the Bio.Fasta.Record object differs from the SeqRecord.
+
+from Bio import Fasta
+handle = open("example.fas")
+for record in Fasta.Iterator(handle, Fasta.RecordParser()) :
+ #record is a Bio.Fasta.Record object
+ print record.title #The full title line as a string
+ print record.sequence #The sequence as a string
+handle.close()
+
+Using Bio.SeqIO instead this becomes:
+
+from Bio import SeqIO
+handle = open("example.fas")
+for seq_record in SeqIO.parse(handle, "fasta") :
+ print seq_record.description #The full title line as a string
+ print seq_record.seq.tostring() #The sequence as a string
+handle.close()
+
+
+
+"""
+from Bio import Seq
+from Bio import SeqRecord
+from Bio import Alphabet
+
+
+class Record:
+ """Holds information from a FASTA record.
+
+ Members:
+ title Title line ('>' character not included).
+ sequence The sequence.
+
+ """
+ def __init__(self, colwidth=60):
+ """__init__(self, colwidth=60)
+
+ Create a new Record. colwidth specifies the number of residues
+ to put on each line when generating FASTA format.
+
+ """
+ self.title = ''
+ self.sequence = ''
+ self._colwidth = colwidth
+
+ def __str__(self):
+ s = []
+ s.append('>%s' % self.title)
+ i = 0
+ while i < len(self.sequence):
+ s.append(self.sequence[i:i+self._colwidth])
+ i = i + self._colwidth
+ #Was having a problem getting the tests to pass on windows...
+ #return os.linesep.join(s)
+ return "\n".join(s)
+
+class Iterator:
+ """Returns one record at a time from a FASTA file.
+ """
+ def __init__(self, handle, parser = None, debug = 0):
+ """Initialize a new iterator.
+ """
+ self.handle = handle
+ self._parser = parser
+ self._debug = debug
+
+ #Skip any text before the first record (e.g. blank lines)
+ while True :
+ line = handle.readline()
+ if not line or line[0] == ">" :
+ break
+ if debug : print "Skipping: " + line
+ self._lookahead = line
+
+ def __iter__(self):
+ return iter(self.next, None)
+
+ def next(self):
+ """Return the next record in the file"""
+ line = self._lookahead
+ if not line:
+ return None
+ assert line[0]==">", line
+ lines = [line.rstrip()]
+ line = self.handle.readline()
+ while line:
+ if line[0] == ">": break
+ if line[0] == "#" :
+ if self._debug : print "Ignoring comment line"
+ pass
+ else :
+ lines.append(line.rstrip())
+ line = self.handle.readline()
+ self._lookahead = line
+ if self._debug : print "Debug: '%s' and '%s'" % (title, "".join(lines))
+ if self._parser is None:
+ return "\n".join(lines)
+ else :
+ return self._parser.parse_string("\n".join(lines))
+
+class RecordParser:
+ """Parses FASTA sequence data into a Fasta.Record object.
+ """
+ def __init__(self, debug = 0):
+ pass
+
+ def parse_string(self, text) :
+ text = text.replace("\r\n","\n") #Crude way of dealing with \r\n
+ assert text[0] == ">", text
+ text = text.split("\n>",1)[0] # Only do the first record if more than one
+ title, sequence = text.split("\n", 1)
+ title = title[1:]
+ rec = Record()
+ rec.title = title
+ rec.sequence = sequence.replace("\n","")
+ return rec
+
+ def parse(self, handle):
+ return self.parse_string(handle.read())
+
+class SequenceParser:
+ """Parses FASTA sequence data into a SeqRecord object.
+ """
+ def __init__(self, alphabet = Alphabet.generic_alphabet, title2ids = None,
+ debug = 0):
+ """Initialize a Scanner and Sequence Consumer.
+
+ Arguments:
+ o alphabet - The alphabet of the sequences to be parsed. If not
+ passed, this will be set as generic_alphabet.
+ o title2ids - A function that, when given the title of the FASTA
+ file (without the beginning >), will return the id, name and
+ description (in that order) for the record. If this is not given,
+ then the entire title line will be used as the description.
+ """
+ self.alphabet = alphabet
+ self.title2ids = title2ids
+
+ def parse_string(self, text) :
+ text = text.replace("\r\n","\n") #Crude way of dealing with \r\n
+ assert text[0] == ">", text
+ text = text.split("\n>",1)[0] # Only do the first record if more than one
+ title, sequence = text.split("\n", 1)
+ title = title[1:]
+
+ seq = Seq.Seq(sequence.replace("\n",""), self.alphabet)
+ rec = SeqRecord.SeqRecord(seq)
+
+ if self.title2ids:
+ seq_id, name, descr = self.title2ids(title)
+ rec.id = seq_id
+ rec.name = name
+ rec.description = descr
+ else:
+ rec.description = title
+
+ return rec
+
+ def parse(self, handle):
+ return self.parse_string(handle.read())
--- /dev/null
+# Copyright 1999 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code for more fancy file handles.
+
+
+Classes:
+UndoHandle File object decorator with support for undo-like operations.
+StringHandle Wraps a file object around a string.
+SGMLHandle File object that automatically strips SGML tags from data.
+
+SGMLStripper Object that strips SGML. This is now considered OBSOLETE, and
+ is likely to be deprecated in a future release of Biopython,
+ and later removed.
+
+"""
+import os
+import StringIO
+import sgmllib
+
+class UndoHandle:
+ """A Python handle that adds functionality for saving lines.
+
+ Saves lines in a LIFO fashion.
+
+ Added methods:
+ saveline Save a line to be returned next time.
+ peekline Peek at the next line without consuming it.
+
+ """
+ def __init__(self, handle):
+ self._handle = handle
+ self._saved = []
+
+ def __iter__(self):
+ return self
+
+ def next(self):
+ next = self.readline()
+ if not next:
+ raise StopIteration
+ return next
+
+ def readlines(self, *args, **keywds):
+ lines = self._saved + self._handle.readlines(*args,**keywds)
+ self._saved = []
+ return lines
+
+ def readline(self, *args, **keywds):
+ if self._saved:
+ line = self._saved.pop(0)
+ else:
+ line = self._handle.readline(*args,**keywds)
+ return line
+
+ def read(self, size=-1):
+ if size == -1:
+ saved = "".join(self._saved)
+ self._saved[:] = []
+ else:
+ saved = ''
+ while size > 0 and self._saved:
+ if len(self._saved[0]) <= size:
+ size = size - len(self._saved[0])
+ saved = saved + self._saved.pop(0)
+ else:
+ saved = saved + self._saved[0][:size]
+ self._saved[0] = self._saved[0][size:]
+ size = 0
+ return saved + self._handle.read(size)
+
+ def saveline(self, line):
+ if line:
+ self._saved = [line] + self._saved
+
+ def peekline(self):
+ if self._saved:
+ line = self._saved[0]
+ else:
+ line = self._handle.readline()
+ self.saveline(line)
+ return line
+
+ def tell(self):
+ lengths = map(len, self._saved)
+ sum = reduce(lambda x, y: x+y, lengths, 0)
+ return self._handle.tell() - sum
+
+ def seek(self, *args):
+ self._saved = []
+ self._handle.seek(*args)
+
+ def __getattr__(self, attr):
+ return getattr(self._handle, attr)
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, type, value, traceback):
+ self._handle.close()
+
+
+# I could make this faster by using cStringIO.
+# However, cStringIO (in v1.52) does not implement the
+# readlines method.
+StringHandle = StringIO.StringIO
+
+
+
+class SGMLHandle:
+ """A Python handle that automatically strips SGML tags from data (OBSOLETE).
+
+ This module is now considered to be obsolete, and is likely to be
+ deprecated in a future release of Biopython, and later removed.
+ """
+ def __init__(self, handle):
+ """SGMLStripper(handle)
+
+ handle is a file handle to SGML-formatted data.
+
+ """
+ self._handle = handle
+ self._stripper = SGMLStripper()
+
+ def read(self, *args, **keywds):
+ data = self._handle.read(*args, **keywds)
+ return self._stripper.strip(data)
+
+ def readline(self, *args, **keywds):
+ line = self._handle.readline(*args, **keywds)
+ return self._stripper.strip(line)
+
+ def readlines(self, *args, **keywds):
+ lines = self._handle.readlines(*args, **keywds)
+ for i in range(len(lines)):
+ lines[i] = self._stripper.strip(str)
+ return lines
+
+ def __getattr__(self, attr):
+ return getattr(self._handle, attr)
+
+
+class SGMLStripper:
+ class MyParser(sgmllib.SGMLParser):
+ def __init__(self):
+ sgmllib.SGMLParser.__init__(self)
+ self.data = ''
+ def handle_data(self, data):
+ self.data = self.data + data
+
+ def __init__(self):
+ self._parser = SGMLStripper.MyParser()
+
+ def strip(self, str):
+ """S.strip(str) -> string
+
+ Strip the SGML tags from str.
+
+ """
+ if not str: # empty string, don't do anything.
+ return ''
+ # I need to make sure that I don't return an empty string if
+ # the buffer is not empty. This can happen if there's a newline
+ # character embedded within a tag. Thus, I'll first check to
+ # see if the last character is a newline. If it is, and it's stripped
+ # away, I'll add it back.
+ is_newline = str[-1] in ['\n', '\r']
+
+ self._parser.data = '' # clear the parser's data (don't reset)
+ self._parser.feed(str)
+ if self._parser.data:
+ str = self._parser.data
+ elif is_newline:
+ str = '\n'
+ else:
+ str = ''
+ return str
+
--- /dev/null
+# Copyright 2001 by Katharine Lindner. All rights reserved.\r
+# This code is part of the Biopython distribution and governed by its\r
+# license. Please see the LICENSE file that should have been included\r
+# as part of this package.\r
+\r
+"""Code for more fancy file handles (OBSOLETE).\r
+\r
+Classes:\r
+Filtered is a decorator for File that allows the user to filter the output\r
+on a line by line basis.\r
+\r
+The FilteredReader module reads a file and applies a sequence of filters to the input\r
+The constructor sets a default filter chain, but the user can select another filter by setting\r
+Bio.FilteredReader.filter_chain.\r
+\r
+handle = open( "filename" )\r
+filtered_reader = Bio.FilteredReader( handle )\r
+filtered_reader.filter_chain = [ remove_asterisks, replace_dot_with_dash ]\r
+filtered_reasder.read()\r
+\r
+All filters in the chain must provide the same interface with a line of text as the single\r
+input parameter and altered text as the return value.\r
+\r
+This module is now considered to be obsolete, and is likely to be deprecated\r
+in a future release of Biopython, and later removed.\r
+"""\r
+\r
+\r
+def dump_saved( name, text, j ):\r
+ """Used for debugging."""\r
+ dump_file = open( name + '%d' % j, "w" )\r
+ k = 0\r
+ for i in range ( 0, len( text ), 80 ):\r
+ dump_file.write( '%s\n' % text[ i : i + 80 ] )\r
+ dump_file.close()\r
+\r
+def remove_leading_whitespace( line ):\r
+ return line.lstrip()\r
+\r
+\r
+def remove_empty_line( line ):\r
+ stripped_line = line.strip()\r
+ if( stripped_line ):\r
+ return line[ : ]\r
+ else:\r
+ return ''\r
+\r
+def remove_useless_dot( line ):\r
+ before = line\r
+ while( 1 ):\r
+ after = before.replace( "\t.\t", "\t\t" )\r
+ if( len( before ) == len( after ) ):\r
+ break\r
+ before = after\r
+ if( after.endswith( '.' ) ):\r
+ after = after[ :-1 ]\r
+ return after\r
+\r
+def fix_punctuation( line ):\r
+ line = line.replace( "'", '' )\r
+ line = line.replace( '"', '' )\r
+ line = line.replace( ';', '\t' )\r
+ line = line.replace( 'entryname', 'id' )\r
+# line = line.lower( )\r
+ if( line ):\r
+ return line[ : ]\r
+ else:\r
+ return ''\r
+\r
+\r
+\r
+class FilteredReader:\r
+ def __init__(self, handle ):\r
+ self._handle = handle\r
+ self._start_line = ''\r
+ self._debug_count = 0\r
+ self.filter_chain = [ remove_empty_line, remove_useless_dot, fix_punctuation ]\r
+\r
+ def __getattr__(self, attr):\r
+ return getattr(self._handle, attr)\r
+\r
+\r
+\r
+ def close(self, *args, **keywds ):\r
+ return self._handle.close( *args, **keywds)\r
+\r
+ def read( self, *args, **keywds ):\r
+ line = ''\r
+ len_expected = self._get_len_expected( args, keywds )\r
+ if( len_expected ):\r
+ filtered_text = self.read_block( len_expected )\r
+ else:\r
+ filtered_text = self.read_to_end()\r
+ return filtered_text\r
+\r
+ def read_block( self, len_expected ):\r
+\r
+ len_filtered = 0\r
+ len_adjusted -= len( self._start_line )\r
+ filtered_text = ''\r
+ while( len_filtered < len_expected ):\r
+\r
+ text_read = self._handle.read( len_adjusted )\r
+ full_text = self._start_line + text_read\r
+ lines = full_text.splitlines( 1 )\r
+ if( text_read == '' ):\r
+ filtered_text = filtered_text + self.filter( lines )\r
+ break\r
+ else:\r
+ all_but_last_line = lines[ :-1 ]\r
+ self._start_line = lines[ -1 ]\r
+ filtered_text = filtered_text + self.filter( all_but_last_line )\r
+ len_filtered_text = len( filtered_text )\r
+ len_adjusted = len_adjusted - len_filtered_text\r
+ return filtered_text[ : ]\r
+\r
+ def read_to_end( self ):\r
+ filtered_text = ''\r
+ text_read = self._handle.read()\r
+ full_text = self._start_line + text_read\r
+ lines = full_text.splitlines( 1 )\r
+ filtered_text += self.filter( lines[:] )\r
+ return filtered_text[ : ]\r
+\r
+ def _get_len_expected( self, args, keywds ):\r
+\r
+ if( len( args) > 0 ):\r
+ len_expected = args[ 0 ]\r
+ if( len_expected < 0 ):\r
+ len_expected = None\r
+ elif 'size' in keywds:\r
+ len_expected = keywds['size']\r
+ else:\r
+ len_expected = None\r
+ return len_expected\r
+\r
+ def filter( self, lines ):\r
+ filter_chain = self.filter_chain\r
+ filtered_text = ''\r
+ for line in lines:\r
+ for filter in filter_chain:\r
+ line = filter( *( line, ) )\r
+ filtered_text += line\r
+\r
+ return filtered_text\r
+\r
+def has_trailing_linefeed( line ):\r
+ if( line.endswith( chr( 13 ) ) or \\r
+ line.endswith( chr( 10 ) ) ):\r
+ return 1\r
+ else:\r
+ return 0\r
--- /dev/null
+# Copyright 2002 by Katharine Lindner. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""handles true random numbers supplied from the the web server of fourmilab. Based on atmospheric noise. The motivation is to support biosimulations that rely on random numbers.
+"""
+
+import urllib
+
+
+def hex_convert(text):
+ import warnings
+ warnings.warn("The function Bio.HotRand.hex_convert is deprecated. Instead of Bio.HotRand.hex_convert(text), please use int(text, 16) instead", DeprecationWarning)
+ return int(text, 16)
+
+def byte_concat( text ):
+ val = 0
+ numbytes = len( text )
+ for i in range( 0, numbytes ):
+ val = val * 256
+ val = val + ord( text[ i ] )
+
+ return val
+
+class HotCache:
+
+ def __init__( self ):
+# self.url = 'http://www.fourmilab.ch/cgi-bin/uncgi/Hotbits?num=5000&min=1&max=6&col=1'
+ self.url = 'http://www.random.org/cgi-bin/randbyte?'
+ self.query = { 'nbytes' : 128, 'fmt' : 'h' }
+ self.fill_hot_cache()
+
+ def fill_hot_cache( self ):
+ url = self.url + urllib.urlencode( self.query )
+ fh = urllib.urlopen( url )
+ self.hot_cache = fh.read()
+ fh.close()
+
+ def next_num( self, num_digits = 4 ):
+ cache = self.hot_cache
+ numbytes = num_digits / 2
+ if( len( cache ) % numbytes != 0 ):
+ print 'len_cache is %d' % len( cache )
+ raise ValueError
+ if( cache == '' ):
+ self.fill_hot_cache()
+ cache = self.hot_cache
+ hexdigits = cache[ :numbytes ]
+ self.hot_cache = cache[ numbytes: ]
+ return byte_concat( hexdigits )
+
+
+
+class HotRandom:
+
+ def __init__( self ):
+ self.hot_cache = HotCache( )
+
+ def hot_rand( self, high, low = 0 ):
+ span = high - low
+ val = self.hot_cache.next_num()
+ val = ( span * val ) >> 16
+ val = val + low
+ return val
+
+
+if( __name__ == '__main__' ):
+ hot_random = HotRandom()
+ for j in range ( 0, 130 ):
+ print hot_random.hot_rand( 25 )
+ nums = [ '0000', 'abcd', '1234', '5555', '4321', 'aaaa', 'ffff' ]
+ for num in nums:
+ print hex_convert( num )
+
+
+
--- /dev/null
+# Copyright 1999 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Index.py
+
+This module provides a way to create indexes to text files.
+
+Classes:
+Index Dictionary-like class used to store index information.
+
+_ShelveIndex An Index class based on the shelve module.
+_InMemoryIndex An in-memory Index class.
+
+"""
+import os
+import array
+import cPickle
+import shelve
+
+class _ShelveIndex(dict):
+ """An index file wrapped around shelve.
+
+ """
+ # Without a good dbm module installed, this is pretty slow and
+ # generates large files. When generating an index on a FASTA-
+ # formatted file with 82000 sequences (37Mb), the
+ # index 'dat' file is 42Mb and 'dir' file is 8Mb.
+
+ __version = 2
+ __version_key = '__version'
+
+ def __init__(self, indexname, truncate=None):
+ dict.__init__(self)
+ try:
+ if truncate:
+ # In python 1.52 and before, dumbdbm (under shelve)
+ # doesn't clear the old database.
+ files = [indexname + '.dir',
+ indexname + '.dat',
+ indexname + '.bak'
+ ]
+ for file in files:
+ if os.path.exists(file):
+ os.unlink(file)
+ raise Exception("open a new shelf")
+ self.data = shelve.open(indexname, flag='r')
+ except:
+ # No database exists.
+ self.data = shelve.open(indexname, flag='n')
+ self.data[self.__version_key] = self.__version
+ else:
+ # Check to make sure the database is the correct version.
+ version = self.data.get(self.__version_key, None)
+ if version is None:
+ raise IOError("Unrecognized index format")
+ elif version != self.__version:
+ raise IOError("Version %s doesn't match my version %s" \
+ % (version, self.__version))
+
+ def __del__(self):
+ if self.__dict__.has_key('data'):
+ self.data.close()
+
+class _InMemoryIndex(dict):
+ """This creates an in-memory index file.
+
+ """
+ # File Format:
+ # version
+ # key value
+ # [...]
+
+ __version = 3
+ __version_key = '__version'
+
+ def __init__(self, indexname, truncate=None):
+ self._indexname = indexname
+ dict.__init__(self)
+ self.__changed = 0 # the index hasn't changed
+
+ # Remove the database if truncate is true.
+ if truncate and os.path.exists(indexname):
+ os.unlink(indexname)
+ self.__changed = 1
+
+ # Load the database if it exists
+ if os.path.exists(indexname):
+ handle = open(indexname)
+ version = self._toobj(handle.readline().rstrip())
+ if version != self.__version:
+ raise IOError("Version %s doesn't match my version %s" \
+ % (version, self.__version))
+ for line in handle:
+ key, value = line.split()
+ key, value = self._toobj(key), self._toobj(value)
+ self[key] = value
+ self.__changed = 0
+
+ def update(self, dict):
+ self.__changed = 1
+ dict.update(self, dict)
+ def __setitem__(self, key, value):
+ self.__changed = 1
+ dict.__setitem__(self, key, value)
+ def __delitem__(self, key):
+ self.__changed = 1
+ dict.__delitem__(self, key)
+ def clear(self):
+ self.__changed = 1
+ dict.clear(self)
+
+ def __del__(self):
+ if self.__changed:
+ handle = open(self._indexname, 'w')
+ handle.write("%s\n" % self._tostr(self.__version))
+ for key, value in self.items():
+ handle.write("%s %s\n" %
+ (self._tostr(key), self._tostr(value)))
+ handle.close()
+
+ def _tostr(self, obj):
+ # I need a representation of the object that's saveable to
+ # a file that uses whitespace as delimiters. Thus, I'm
+ # going to pickle the object, and then convert each character of
+ # the string to its ASCII integer value. Then, I'm going to convert
+ # the integers into strings and join them together with commas.
+ # It's not the most efficient way of storing things, but it's
+ # relatively fast.
+ s = cPickle.dumps(obj)
+ intlist = array.array('b', s)
+ strlist = map(str, intlist)
+ return ','.join(strlist)
+
+ def _toobj(self, str):
+ intlist = map(int, str.split(','))
+ intlist = array.array('b', intlist)
+ strlist = map(chr, intlist)
+ return cPickle.loads(''.join(strlist))
+
+Index = _InMemoryIndex
--- /dev/null
+#!/usr/bin/env python
+
+"""
+This module provides code for doing logistic regressions.
+
+
+Classes:
+LogisticRegression Holds information for a LogisticRegression classifier.
+
+
+Functions:
+train Train a new classifier.
+calculate Calculate the probabilities of each class, given an observation.
+classify Classify an observation into a class.
+"""
+
+#TODO - Remove this work around once we drop python 2.3 support
+try:
+ set = set
+except NameError:
+ from sets import Set as set
+
+#from numpy import *
+#from numpy.linalg import *
+import numpy
+import numpy.linalg
+
+class LogisticRegression:
+ """Holds information necessary to do logistic regression
+ classification.
+
+ Members:
+ beta List of the weights for each dimension.
+
+ """
+ def __init__(self):
+ """LogisticRegression()"""
+ self.beta = []
+
+def train(xs, ys, update_fn=None, typecode=None):
+ """train(xs, ys[, update_fn]) -> LogisticRegression
+
+ Train a logistic regression classifier on a training set. xs is a
+ list of observations and ys is a list of the class assignments,
+ which should be 0 or 1. xs and ys should contain the same number
+ of elements. update_fn is an optional callback function that
+ takes as parameters that iteration number and log likelihood.
+
+ """
+ if len(xs) != len(ys):
+ raise ValueError("xs and ys should be the same length.")
+ classes = set(ys)
+ if classes != set([0, 1]):
+ raise ValueError("Classes should be 0's and 1's")
+ if typecode is None:
+ typecode = 'd'
+
+ # Dimensionality of the data is the dimensionality of the
+ # observations plus a constant dimension.
+ N, ndims = len(xs), len(xs[0]) + 1
+ if N==0 or ndims==1:
+ raise ValueError("No observations or observation of 0 dimension.")
+
+ # Make an X array, with a constant first dimension.
+ X = numpy.ones((N, ndims), typecode)
+ X[:, 1:] = xs
+ Xt = numpy.transpose(X)
+ y = numpy.asarray(ys, typecode)
+
+ # Initialize the beta parameter to 0.
+ beta = numpy.zeros(ndims, typecode)
+
+ MAX_ITERATIONS = 500
+ CONVERGE_THRESHOLD = 0.01
+ stepsize = 1.0
+ # Now iterate using Newton-Raphson until the log-likelihoods
+ # converge.
+ iter = 0
+ old_beta = old_llik = None
+ while iter < MAX_ITERATIONS:
+ # Calculate the probabilities. p = e^(beta X) / (1+e^(beta X))
+ ebetaX = numpy.exp(numpy.dot(beta, Xt))
+ p = ebetaX / (1+ebetaX)
+
+ # Find the log likelihood score and see if I've converged.
+ logp = y*numpy.log(p) + (1-y)*numpy.log(1-p)
+ llik = sum(logp)
+ if update_fn is not None:
+ update_fn(iter, llik)
+ # Check to see if the likelihood decreased. If it did, then
+ # restore the old beta parameters and half the step size.
+ if llik < old_llik:
+ stepsize = stepsize / 2.0
+ beta = old_beta
+ # If I've converged, then stop.
+ if old_llik is not None and numpy.fabs(llik-old_llik) <= CONVERGE_THRESHOLD:
+ break
+ old_llik, old_beta = llik, beta
+ iter += 1
+
+ W = numpy.identity(N) * p
+ Xtyp = numpy.dot(Xt, y-p) # Calculate the first derivative.
+ XtWX = numpy.dot(numpy.dot(Xt, W), X) # Calculate the second derivative.
+ #u, s, vt = singular_value_decomposition(XtWX)
+ #print "U", u
+ #print "S", s
+ delta = numpy.linalg.solve(XtWX, Xtyp)
+ if numpy.fabs(stepsize-1.0) > 0.001:
+ delta = delta * stepsize
+ beta = beta + delta # Update beta.
+ else:
+ raise RuntimeError("Didn't converge.")
+
+ lr = LogisticRegression()
+ lr.beta = map(float, beta) # Convert back to regular array.
+ return lr
+
+def calculate(lr, x):
+ """calculate(lr, x) -> list of probabilities
+
+ Calculate the probability for each class. lr is a
+ LogisticRegression object. x is the observed data. Returns a
+ list of the probability that it fits each class.
+
+ """
+ # Insert a constant term for x.
+ x = numpy.asarray([1.0] + x)
+ # Calculate the probability. p = e^(beta X) / (1+e^(beta X))
+ ebetaX = numpy.exp(numpy.dot(lr.beta, x))
+ p = ebetaX / (1+ebetaX)
+ return [1-p, p]
+
+def classify(lr, x):
+ """classify(lr, x) -> 1 or 0
+
+ Classify an observation into a class.
+
+ """
+ probs = calculate(lr, x)
+ if probs[0] > probs[1]:
+ return 0
+ return 1
--- /dev/null
+# Copyright 1999 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code to support writing parsers.
+
+
+
+Classes:
+AbstractParser Base class for parsers.
+AbstractConsumer Base class of all Consumers.
+TaggingConsumer Consumer that tags output with its event. For debugging
+SGMLStrippingConsumer Consumer that strips SGML tags from output.
+EventGenerator Generate Biopython Events from Martel XML output
+ (note that Martel is now DEPRECATED)
+
+Functions:
+safe_readline Read a line from a handle, with check for EOF.
+safe_peekline Peek at next line, with check for EOF.
+read_and_call Read a line from a handle and pass it to a method.
+read_and_call_while Read many lines, as long as a condition is met.
+read_and_call_until Read many lines, until a condition is met.
+attempt_read_and_call Like read_and_call, but forgiving of errors.
+is_blank_line Test whether a line is blank.
+
+"""
+
+import sys
+import traceback
+from types import *
+
+from Bio import File
+
+# XML from python 2.0
+try:
+ from xml.sax import handler
+ xml_support = 1
+except ImportError:
+ sys.stderr.write("Warning: Could not import SAX for dealing with XML.\n" +
+ "This causes problems with some ParserSupport modules\n")
+ xml_support = 0
+
+class AbstractParser:
+ """Base class for other parsers.
+
+ """
+ def parse(self, handle):
+ raise NotImplementedError("Please implement in a derived class")
+
+ def parse_str(self, string):
+ return self.parse(File.StringHandle(string))
+
+ def parse_file(self, filename):
+ h = open(filename)
+ try:
+ retval = self.parse(h)
+ finally:
+ h.close()
+ return retval
+
+class AbstractConsumer:
+ """Base class for other Consumers.
+
+ Derive Consumers from this class and implement appropriate
+ methods for each event that you want to receive.
+
+ """
+ def _unhandled_section(self):
+ pass
+ def _unhandled(self, data):
+ pass
+ def __getattr__(self, attr):
+ if attr[:6] == 'start_' or attr[:4] == 'end_':
+ method = self._unhandled_section
+ else:
+ method = self._unhandled
+ return method
+
+class TaggingConsumer(AbstractConsumer):
+ """A Consumer that tags the data stream with the event and
+ prints it to a handle. Useful for debugging.
+
+ """
+ def __init__(self, handle=None, colwidth=15, maxwidth=80):
+ """TaggingConsumer(handle=sys.stdout, colwidth=15, maxwidth=80)"""
+ # I can't assign sys.stdout to handle in the argument list.
+ # If I do that, handle will be assigned the value of sys.stdout
+ # the first time this function is called. This will fail if
+ # the user has assigned sys.stdout to some other file, which may
+ # be closed or invalid at a later time.
+ if handle is None:
+ handle = sys.stdout
+ self._handle = handle
+ self._colwidth = colwidth
+ self._maxwidth = maxwidth
+
+ def unhandled_section(self):
+ self._print_name('unhandled_section')
+
+ def unhandled(self, data):
+ self._print_name('unhandled', data)
+
+ def _print_name(self, name, data=None):
+ if data is None:
+ # Write the name of a section.
+ self._handle.write("%s %s\n" % ("*"*self._colwidth, name))
+ else:
+ # Write the tag and line.
+ self._handle.write("%-*s: %s\n" % (
+ self._colwidth, name[:self._colwidth],
+ data[:self._maxwidth-self._colwidth-2].rstrip()))
+
+ def __getattr__(self, attr):
+ if attr[:6] == 'start_' or attr[:4] == 'end_':
+ method = lambda a=attr, s=self: s._print_name(a)
+ else:
+ method = lambda x, a=attr, s=self: s._print_name(a, x)
+ return method
+
+class SGMLStrippingConsumer:
+ """A consumer that strips off SGML tags.
+
+ This is meant to be used as a decorator for other consumers.
+
+ """
+ def __init__(self, consumer):
+ if type(consumer) is not InstanceType:
+ raise ValueError("consumer should be an instance")
+ self._consumer = consumer
+ self._prev_attr = None
+ self._stripper = File.SGMLStripper()
+
+ def _apply_clean_data(self, data):
+ clean = self._stripper.strip(data)
+ self._prev_attr(clean)
+
+ def __getattr__(self, name):
+ if name in ['_prev_attr', '_stripper']:
+ return getattr(self, name)
+ attr = getattr(self._consumer, name)
+ # If this is not a method, then return it as is.
+ if type(attr) is not MethodType:
+ return attr
+ # If it's a section method, then return it.
+ if name[:6] == 'start_' or name[:4] == 'end_':
+ return attr
+ # Otherwise, it's an info event, and return my method.
+ self._prev_attr = attr
+ return self._apply_clean_data
+
+# onle use the Event Generator if XML handling is okay
+if xml_support:
+ class EventGenerator(handler.ContentHandler):
+ """Handler to generate events associated with a Martel parsed file.
+
+ This acts like a normal SAX handler, and accepts XML generated by
+ Martel during parsing. These events are then converted into
+ 'Biopython events', which can then be caught by a standard
+ biopython consumer.
+
+ Note that Martel is now DEPRECATED.
+ """
+ def __init__(self, consumer, interest_tags, callback_finalizer = None,
+ exempt_tags = []):
+ """Initialize to begin catching and firing off events.
+
+ Arguments:
+ o consumer - The consumer that we'll send Biopython events to.
+
+ o interest_tags - A listing of all the tags we are interested in.
+
+ o callback_finalizer - A function to deal with the collected
+ information before passing it on to the consumer. By default
+ the collected information is a list of all of the lines read
+ for a particular tag -- if there are multiple tags in a row
+ like:
+
+ <some_info>Spam<some_info>
+ <some_info>More Spam<some_info>
+
+ In this case the list of information would be:
+
+ ['Spam', 'More Spam']
+
+ This list of lines will be passed to the callback finalizer if
+ it is present. Otherwise the consumer will be called with the
+ list of content information.
+
+ o exempt_tags - A listing of particular tags that are exempt from
+ being processed by the callback_finalizer. This allows you to
+ use a finalizer to deal with most tags, but leave those you don't
+ want touched.
+ """
+ self._consumer = consumer
+ self.interest_tags = interest_tags
+ self._finalizer = callback_finalizer
+ self._exempt_tags = exempt_tags
+
+ # a dictionary of content for each tag of interest
+ # the information for each tag is held as a list of the lines.
+ # This allows us to collect information from multiple tags
+ # in a row, and return it all at once.
+ self.info = {}
+ for tag in self.interest_tags:
+ self.info[tag] = []
+
+ # the previous tag we were collecting information for.
+ # We set a delay in sending info to the consumer so that we can
+ # collect a bunch of tags in a row and append all of the info
+ # together.
+ self._previous_tag = ''
+
+ # the current character information for a tag
+ self._cur_content = []
+ # whether we should be collecting information
+ self._collect_characters = 0
+
+ def startElement(self, name, attrs):
+ """Determine if we should collect characters from this tag.
+ """
+ if name in self.interest_tags:
+ self._collect_characters = 1
+
+ def characters(self, content):
+ """Extract the information if we are interested in it.
+ """
+ if self._collect_characters:
+ self._cur_content.append(content)
+
+ def endElement(self, name):
+ """Send the information to the consumer.
+
+ Once we've got the end element we've collected up all of the
+ character information we need, and we need to send this on to
+ the consumer to do something with it.
+
+ We have a delay of one tag on doing this, so that we can collect
+ all of the info from multiple calls to the same element at once.
+ """
+ # only deal with the tag if it is something we are
+ # interested in and potentially have information for
+ if self._collect_characters:
+ # add all of the information collected inside this tag
+ self.info[name].append("".join(self._cur_content))
+ # reset our information and flags
+ self._cur_content = []
+ self._collect_characters = 0
+
+ # if we are at a new tag, pass on the info from the last tag
+ if self._previous_tag and self._previous_tag != name:
+ self._make_callback(self._previous_tag)
+
+ # set this tag as the next to be passed
+ self._previous_tag = name
+
+ def _make_callback(self, name):
+ """Call the callback function with the info with the given name.
+ """
+ # strip off whitespace and call the consumer
+ callback_function = getattr(self._consumer, name)
+
+ # --- pass back the information
+ # if there is a finalizer, use that
+ if self._finalizer is not None and name not in self._exempt_tags:
+ info_to_pass = self._finalizer(self.info[name])
+ # otherwise pass back the entire list of information
+ else:
+ info_to_pass = self.info[name]
+
+ callback_function(info_to_pass)
+
+ # reset the information for the tag
+ self.info[name] = []
+
+ def endDocument(self):
+ """Make sure all of our information has been passed.
+
+ This just flushes out any stored tags that need to be passed.
+ """
+ if self._previous_tag:
+ self._make_callback(self._previous_tag)
+
+def read_and_call(uhandle, method, **keywds):
+ """read_and_call(uhandle, method[, start][, end][, contains][, blank][, has_re])
+
+ Read a line from uhandle, check it, and pass it to the method.
+ Raises a ValueError if the line does not pass the checks.
+
+ start, end, contains, blank, and has_re specify optional conditions
+ that the line must pass. start and end specifies what the line must
+ begin or end with (not counting EOL characters). contains
+ specifies a substring that must be found in the line. If blank
+ is a true value, then the line must be blank. has_re should be
+ a regular expression object with a pattern that the line must match
+ somewhere.
+
+ """
+ line = safe_readline(uhandle)
+ errmsg = _fails_conditions(*(line,), **keywds)
+ if errmsg is not None:
+ raise ValueError(errmsg)
+ method(line)
+
+def read_and_call_while(uhandle, method, **keywds):
+ """read_and_call_while(uhandle, method[, start][, end][, contains][, blank][, has_re]) -> number of lines
+
+ Read a line from uhandle and pass it to the method as long as
+ some condition is true. Returns the number of lines that were read.
+
+ See the docstring for read_and_call for a description of the parameters.
+
+ """
+ nlines = 0
+ while 1:
+ line = safe_readline(uhandle)
+ # If I've failed the condition, then stop reading the line.
+ if _fails_conditions(*(line,), **keywds):
+ uhandle.saveline(line)
+ break
+ method(line)
+ nlines = nlines + 1
+ return nlines
+
+def read_and_call_until(uhandle, method, **keywds):
+ """read_and_call_until(uhandle, method,
+ start=None, end=None, contains=None, blank=None) -> number of lines
+
+ Read a line from uhandle and pass it to the method until
+ some condition is true. Returns the number of lines that were read.
+
+ See the docstring for read_and_call for a description of the parameters.
+
+ """
+ nlines = 0
+ while 1:
+ line = safe_readline(uhandle)
+ # If I've met the condition, then stop reading the line.
+ if not _fails_conditions(*(line,), **keywds):
+ uhandle.saveline(line)
+ break
+ method(line)
+ nlines = nlines + 1
+ return nlines
+
+def attempt_read_and_call(uhandle, method, **keywds):
+ """attempt_read_and_call(uhandle, method, **keywds) -> boolean
+
+ Similar to read_and_call, but returns a boolean specifying
+ whether the line has passed the checks. Does not raise
+ exceptions.
+
+ See docs for read_and_call for a description of the function
+ arguments.
+
+ """
+ line = safe_readline(uhandle)
+ passed = not _fails_conditions(*(line,), **keywds)
+ if passed:
+ method(line)
+ else:
+ uhandle.saveline(line)
+ return passed
+
+def _fails_conditions(line, start=None, end=None, contains=None, blank=None,
+ has_re=None):
+ if start is not None:
+ if line[:len(start)] != start:
+ return "Line does not start with '%s':\n%s" % (start, line)
+ if end is not None:
+ if line.rstrip()[-len(end):] != end:
+ return "Line does not end with '%s':\n%s" % (end, line)
+ if contains is not None:
+ if line.find(contains) == -1:
+ return "Line does not contain '%s':\n%s" % (contains, line)
+ if blank is not None:
+ if blank:
+ if not is_blank_line(line):
+ return "Expected blank line, but got:\n%s" % line
+ else:
+ if is_blank_line(line):
+ return "Expected non-blank line, but got a blank one"
+ if has_re is not None:
+ if has_re.search(line) is None:
+ return "Line does not match regex '%s':\n%s" % (
+ has_re.pattern, line)
+ return None
+
+def is_blank_line(line, allow_spaces=0):
+ """is_blank_line(line, allow_spaces=0) -> boolean
+
+ Return whether a line is blank. allow_spaces specifies whether to
+ allow whitespaces in a blank line. A true value signifies that a
+ line containing whitespaces as well as end-of-line characters
+ should be considered blank.
+
+ """
+ if not line:
+ return 1
+ if allow_spaces:
+ return line.rstrip() == ''
+ return line[0] == '\n' or line[0] == '\r'
+
+def safe_readline(handle):
+ """safe_readline(handle) -> line
+
+ Read a line from an UndoHandle and return it. If there are no more
+ lines to read, I will raise a ValueError.
+
+ """
+ line = handle.readline()
+ if not line:
+ raise ValueError("Unexpected end of stream.")
+ return line
+
+def safe_peekline(handle):
+ """safe_peekline(handle) -> line
+
+ Peek at the next line in an UndoHandle and return it. If there are no
+ more lines to peek, I will raise a ValueError.
+
+ """
+ line = handle.peekline()
+ if not line:
+ raise ValueError("Unexpected end of stream.")
+ return line
--- /dev/null
+"""Third party and other parsers useful internally to Biopython.
+"""
--- /dev/null
+# Copyright (c) 1998-2000 John Aycock
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+__version__ = 'SPARK-0.6.1'
+
+import re
+import sys
+
+def _namelist(instance):
+ namelist, namedict, classlist = [], {}, [instance.__class__]
+ for c in classlist:
+ for b in c.__bases__:
+ classlist.append(b)
+ for name in dir(c):
+ if name not in namedict:
+ namelist.append(name)
+ namedict[name] = 1
+ return namelist
+
+class GenericScanner:
+ def __init__(self):
+ pattern = self.reflect()
+ self.re = re.compile(pattern, re.VERBOSE)
+
+ self.index2func = {}
+ for name, number in self.re.groupindex.items():
+ self.index2func[number-1] = getattr(self, 't_' + name)
+
+ def makeRE(self, name):
+ doc = getattr(self, name).__doc__
+ rv = '(?P<%s>%s)' % (name[2:], doc)
+ return rv
+
+ def reflect(self):
+ rv = []
+ for name in _namelist(self):
+ if name[:2] == 't_' and name != 't_default':
+ rv.append(self.makeRE(name))
+
+ rv.append(self.makeRE('t_default'))
+ return '|'.join(rv)
+
+ def error(self, s, pos):
+ print "Lexical error at position %s" % pos
+ raise SystemExit
+
+ def tokenize(self, s):
+ pos = 0
+ n = len(s)
+ while pos < n:
+ m = self.re.match(s, pos)
+ if m is None:
+ self.error(s, pos)
+
+ groups = m.groups()
+ for i in range(len(groups)):
+ if groups[i] and i in self.index2func:
+ self.index2func[i](groups[i])
+ pos = m.end()
+
+ def t_default(self, s):
+ r'( . | \n )+'
+ pass
+
+class GenericParser:
+ def __init__(self, start):
+ self.rules = {}
+ self.rule2func = {}
+ self.rule2name = {}
+ self.collectRules()
+ self.startRule = self.augment(start)
+ self.ruleschanged = 1
+
+ _START = 'START'
+ _EOF = 'EOF'
+
+ #
+ # A hook for GenericASTBuilder and GenericASTMatcher.
+ #
+ def preprocess(self, rule, func): return rule, func
+
+ def addRule(self, doc, func):
+ rules = doc.split()
+
+ index = []
+ for i in range(len(rules)):
+ if rules[i] == '::=':
+ index.append(i-1)
+ index.append(len(rules))
+
+ for i in range(len(index)-1):
+ lhs = rules[index[i]]
+ rhs = rules[index[i]+2:index[i+1]]
+ rule = (lhs, tuple(rhs))
+
+ rule, fn = self.preprocess(rule, func)
+
+ if lhs in self.rules:
+ self.rules[lhs].append(rule)
+ else:
+ self.rules[lhs] = [ rule ]
+ self.rule2func[rule] = fn
+ self.rule2name[rule] = func.__name__[2:]
+ self.ruleschanged = 1
+
+ def collectRules(self):
+ for name in _namelist(self):
+ if name[:2] == 'p_':
+ func = getattr(self, name)
+ doc = func.__doc__
+ self.addRule(doc, func)
+
+ def augment(self, start):
+ #
+ # Tempting though it is, this isn't made into a call
+ # to self.addRule() because the start rule shouldn't
+ # be subject to preprocessing.
+ #
+ startRule = (self._START, ( start, self._EOF ))
+ self.rule2func[startRule] = lambda args: args[0]
+ self.rules[self._START] = [ startRule ]
+ self.rule2name[startRule] = ''
+ return startRule
+
+ def makeFIRST(self):
+ union = {}
+ self.first = {}
+
+ for rulelist in self.rules.values():
+ for lhs, rhs in rulelist:
+ if lhs not in self.first:
+ self.first[lhs] = {}
+
+ if len(rhs) == 0:
+ self.first[lhs][None] = 1
+ continue
+
+ sym = rhs[0]
+ if sym not in self.rules:
+ self.first[lhs][sym] = 1
+ else:
+ union[(sym, lhs)] = 1
+ changes = 1
+ while changes:
+ changes = 0
+ for src, dest in union.keys():
+ destlen = len(self.first[dest])
+ self.first[dest].update(self.first[src])
+ if len(self.first[dest]) != destlen:
+ changes = 1
+
+ #
+ # An Earley parser, as per J. Earley, "An Efficient Context-Free
+ # Parsing Algorithm", CACM 13(2), pp. 94-102. Also J. C. Earley,
+ # "An Efficient Context-Free Parsing Algorithm", Ph.D. thesis,
+ # Carnegie-Mellon University, August 1968, p. 27.
+ #
+
+ def typestring(self, token):
+ return None
+
+ def error(self, token):
+ print "Syntax error at or near `%s' token" % token
+ raise SystemExit
+
+ def parse(self, tokens):
+ tree = {}
+ tokens.append(self._EOF)
+ states = { 0: [ (self.startRule, 0, 0) ] }
+
+ if self.ruleschanged:
+ self.makeFIRST()
+
+ for i in xrange(len(tokens)):
+ states[i+1] = []
+
+ if states[i] == []:
+ break
+ self.buildState(tokens[i], states, i, tree)
+
+ #_dump(tokens, states)
+
+ if i < len(tokens)-1 or states[i+1] != [(self.startRule, 2, 0)]:
+ del tokens[-1]
+ self.error(tokens[i-1])
+ rv = self.buildTree(tokens, tree, ((self.startRule, 2, 0), i+1))
+ del tokens[-1]
+ return rv
+
+ def buildState(self, token, states, i, tree):
+ needsCompletion = {}
+ state = states[i]
+ predicted = {}
+
+ for item in state:
+ rule, pos, parent = item
+ lhs, rhs = rule
+
+ #
+ # A -> a . (completer)
+ #
+ if pos == len(rhs):
+ if len(rhs) == 0:
+ needsCompletion[lhs] = (item, i)
+
+ for pitem in states[parent]:
+ if pitem is item:
+ break
+
+ prule, ppos, pparent = pitem
+ plhs, prhs = prule
+
+ if prhs[ppos:ppos+1] == (lhs,):
+ new = (prule,
+ ppos+1,
+ pparent)
+ if new not in state:
+ state.append(new)
+ tree[(new, i)] = [(item, i)]
+ else:
+ tree[(new, i)].append((item, i))
+ continue
+
+ nextSym = rhs[pos]
+
+ #
+ # A -> a . B (predictor)
+ #
+ if nextSym in self.rules:
+ #
+ # Work on completer step some more; for rules
+ # with empty RHS, the "parent state" is the
+ # current state we're adding Earley items to,
+ # so the Earley items the completer step needs
+ # may not all be present when it runs.
+ #
+ if nextSym in needsCompletion:
+ new = (rule, pos+1, parent)
+ olditem_i = needsCompletion[nextSym]
+ if new not in state:
+ state.append(new)
+ tree[(new, i)] = [olditem_i]
+ else:
+ tree[(new, i)].append(olditem_i)
+
+ #
+ # Has this been predicted already?
+ #
+ if nextSym in predicted:
+ continue
+ predicted[nextSym] = 1
+
+ ttype = token is not self._EOF and \
+ self.typestring(token) or \
+ None
+ if ttype is not None:
+ #
+ # Even smarter predictor, when the
+ # token's type is known. The code is
+ # grungy, but runs pretty fast. Three
+ # cases are looked for: rules with
+ # empty RHS; first symbol on RHS is a
+ # terminal; first symbol on RHS is a
+ # nonterminal (and isn't nullable).
+ #
+ for prule in self.rules[nextSym]:
+ new = (prule, 0, i)
+ prhs = prule[1]
+ if len(prhs) == 0:
+ state.append(new)
+ continue
+ prhs0 = prhs[0]
+ if prhs0 not in self.rules:
+ if prhs0 != ttype:
+ continue
+ else:
+ state.append(new)
+ continue
+ first = self.first[prhs0]
+ if None not in first and \
+ ttype not in first:
+ continue
+ state.append(new)
+ continue
+
+ for prule in self.rules[nextSym]:
+ #
+ # Smarter predictor, as per Grune &
+ # Jacobs' _Parsing Techniques_. Not
+ # as good as FIRST sets though.
+ #
+ prhs = prule[1]
+ if len(prhs) > 0 and \
+ prhs[0] not in self.rules and \
+ token != prhs[0]:
+ continue
+ state.append((prule, 0, i))
+
+ #
+ # A -> a . c (scanner)
+ #
+ elif token == nextSym:
+ #assert new not in states[i+1]
+ states[i+1].append((rule, pos+1, parent))
+
+ def buildTree(self, tokens, tree, root):
+ stack = []
+ self.buildTree_r(stack, tokens, -1, tree, root)
+ return stack[0]
+
+ def buildTree_r(self, stack, tokens, tokpos, tree, root):
+ (rule, pos, parent), state = root
+
+ while pos > 0:
+ want = ((rule, pos, parent), state)
+ if want not in tree:
+ #
+ # Since pos > 0, it didn't come from closure,
+ # and if it isn't in tree[], then there must
+ # be a terminal symbol to the left of the dot.
+ # (It must be from a "scanner" step.)
+ #
+ pos = pos - 1
+ state = state - 1
+ stack.insert(0, tokens[tokpos])
+ tokpos = tokpos - 1
+ else:
+ #
+ # There's a NT to the left of the dot.
+ # Follow the tree pointer recursively (>1
+ # tree pointers from it indicates ambiguity).
+ # Since the item must have come about from a
+ # "completer" step, the state where the item
+ # came from must be the parent state of the
+ # item the tree pointer points to.
+ #
+ children = tree[want]
+ if len(children) > 1:
+ child = self.ambiguity(children)
+ else:
+ child = children[0]
+
+ tokpos = self.buildTree_r(stack,
+ tokens, tokpos,
+ tree, child)
+ pos = pos - 1
+ (crule, cpos, cparent), cstate = child
+ state = cparent
+
+ lhs, rhs = rule
+ result = self.rule2func[rule](stack[:len(rhs)])
+ stack[:len(rhs)] = [result]
+ return tokpos
+
+ def ambiguity(self, children):
+ #
+ # XXX - problem here and in collectRules() if the same
+ # rule appears in >1 method. But in that case the
+ # user probably gets what they deserve :-) Also
+ # undefined results if rules causing the ambiguity
+ # appear in the same method.
+ #
+ sortlist = []
+ name2index = {}
+ for i in range(len(children)):
+ ((rule, pos, parent), index) = children[i]
+ lhs, rhs = rule
+ name = self.rule2name[rule]
+ sortlist.append((len(rhs), name))
+ name2index[name] = i
+ sortlist.sort()
+ list = map(lambda (a,b): b, sortlist)
+ return children[name2index[self.resolve(list)]]
+
+ def resolve(self, list):
+ #
+ # Resolve ambiguity in favor of the shortest RHS.
+ # Since we walk the tree from the top down, this
+ # should effectively resolve in favor of a "shift".
+ #
+ return list[0]
+
+#
+# GenericASTBuilder automagically constructs a concrete/abstract syntax tree
+# for a given input. The extra argument is a class (not an instance!)
+# which supports the "__setslice__" and "__len__" methods.
+#
+# XXX - silently overrides any user code in methods.
+#
+
+class GenericASTBuilder(GenericParser):
+ def __init__(self, AST, start):
+ GenericParser.__init__(self, start)
+ self.AST = AST
+
+ def preprocess(self, rule, func):
+ rebind = lambda lhs, self=self: \
+ lambda args, lhs=lhs, self=self: \
+ self.buildASTNode(args, lhs)
+ lhs, rhs = rule
+ return rule, rebind(lhs)
+
+ def buildASTNode(self, args, lhs):
+ children = []
+ for arg in args:
+ if isinstance(arg, self.AST):
+ children.append(arg)
+ else:
+ children.append(self.terminal(arg))
+ return self.nonterminal(lhs, children)
+
+ def terminal(self, token): return token
+
+ def nonterminal(self, type, args):
+ rv = self.AST(type)
+ rv[:len(args)] = args
+ return rv
+
+#
+# GenericASTTraversal is a Visitor pattern according to Design Patterns. For
+# each node it attempts to invoke the method n_<node type>, falling
+# back onto the default() method if the n_* can't be found. The preorder
+# traversal also looks for an exit hook named n_<node type>_exit (no default
+# routine is called if it's not found). To prematurely halt traversal
+# of a subtree, call the prune() method -- this only makes sense for a
+# preorder traversal. Node type is determined via the typestring() method.
+#
+
+class GenericASTTraversalPruningException:
+ pass
+
+class GenericASTTraversal:
+ def __init__(self, ast):
+ self.ast = ast
+
+ def typestring(self, node):
+ return node.type
+
+ def prune(self):
+ raise GenericASTTraversalPruningException
+
+ def preorder(self, node=None):
+ if node is None:
+ node = self.ast
+
+ try:
+ name = 'n_' + self.typestring(node)
+ if hasattr(self, name):
+ func = getattr(self, name)
+ func(node)
+ else:
+ self.default(node)
+ except GenericASTTraversalPruningException:
+ return
+
+ for kid in node:
+ self.preorder(kid)
+
+ name = name + '_exit'
+ if hasattr(self, name):
+ func = getattr(self, name)
+ func(node)
+
+ def postorder(self, node=None):
+ if node is None:
+ node = self.ast
+
+ for kid in node:
+ self.postorder(kid)
+
+ name = 'n_' + self.typestring(node)
+ if hasattr(self, name):
+ func = getattr(self, name)
+ func(node)
+ else:
+ self.default(node)
+
+
+ def default(self, node):
+ pass
+
+#
+# GenericASTMatcher. AST nodes must have "__getitem__" and "__cmp__"
+# implemented.
+#
+# XXX - makes assumptions about how GenericParser walks the parse tree.
+#
+
+class GenericASTMatcher(GenericParser):
+ def __init__(self, start, ast):
+ GenericParser.__init__(self, start)
+ self.ast = ast
+
+ def preprocess(self, rule, func):
+ rebind = lambda func, self=self: \
+ lambda args, func=func, self=self: \
+ self.foundMatch(args, func)
+ lhs, rhs = rule
+ rhslist = list(rhs)
+ rhslist.reverse()
+
+ return (lhs, tuple(rhslist)), rebind(func)
+
+ def foundMatch(self, args, func):
+ func(args[-1])
+ return args[-1]
+
+ def match_r(self, node):
+ self.input.insert(0, node)
+ children = 0
+
+ for child in node:
+ if children == 0:
+ self.input.insert(0, '(')
+ children = children + 1
+ self.match_r(child)
+
+ if children > 0:
+ self.input.insert(0, ')')
+
+ def match(self, ast=None):
+ if ast is None:
+ ast = self.ast
+ self.input = []
+
+ self.match_r(ast)
+ self.parse(self.input)
+
+ def resolve(self, list):
+ #
+ # Resolve ambiguity in favor of the longest RHS.
+ #
+ return list[-1]
+
+def _dump(tokens, states):
+ for i in range(len(states)):
+ print 'state', i
+ for (lhs, rhs), pos, parent in states[i]:
+ print '\t', lhs, '::=',
+ print ' '.join(rhs[:pos]),
+ print '.',
+ print ' '.join(rhs[pos:]),
+ print ',', parent
+ if i < len(tokens):
+ print
+ print 'token', str(tokens[i])
+ print
--- /dev/null
+# Stores properties associated with the class of an object.
+
+
+# Would it be nice to have support for more than one resolver per
+# class? In the meanwhile, they could collude using a dispatch
+# object.
+
+# Do you need access to the actual resolver?
+
+# Resolvers get the sequence because they may do a per-object lookup.
+
+# Could cache search results for better performance.
+
+
+# Dictionary which creates dictionary elements, so lookups never fail.
+# The new elements are always dictionaries.
+class CreateDict(dict):
+ def __getitem__(self, key):
+ return self.setdefault(key,{})
+
+class PropertyManager:
+ def __init__(self):
+ self.class_property = CreateDict()
+ self.class_property_resolver = CreateDict()
+ self.class_resolver = {}
+
+ def resolve(self, obj, property):
+ try:
+ klass = obj.__class__
+ except AttributeError:
+ raise KeyError("built-in instance")
+
+ return self.resolve_class(klass, property)
+
+ def resolve_class(self, klass, property):
+ # Hopefully, we'll find the hit right away
+ try:
+ return self.class_property[klass][property]
+ except KeyError:
+ pass
+
+ # Is there a property resolver?
+ try:
+ return self.class_property_resolver[klass][property](
+ self, klass, property)
+ except KeyError:
+ pass
+
+ # What about the class resolver?
+ try:
+ return self.class_resolver[klass](self, klass, property)
+ except KeyError:
+ pass
+
+ # That failed, so we walk up the class tree, depth-first and
+ # left-to-right (same as Python). For each class, check if
+ # the property exists, then check if the property resolver
+ # exists, and finally, check for the class resolver.
+
+ bases = list(klass.__bases__)
+ while bases:
+ base = bases.pop()
+ try:
+ return self.class_property[base][property]
+ except KeyError:
+ pass
+ try:
+ return self.class_property_resolver[base][property](
+ self, klass, property)
+ except KeyError:
+ pass
+ try:
+ return self.class_resolver[base](self, klass, property)
+ except KeyError:
+ pass
+
+ # this is why the search is depth-first/right-left
+ bases[:0] = list(base.__bases__)
+ raise KeyError("cannot find property %s for class %s" \
+ % (property, klass))
+
+
+default_manager = PropertyManager()
--- /dev/null
+# BLASTN 2.0a19MP-WashU [05-Feb-1998] [Build decunix3.2 01:53:29 05-Feb-1998]
+# BLASTP 2.0.4 [Feb-24-1998]
+class Algorithm:
+ def __init__(self, name, version, description = ""):
+ self.name = name # 'blastx', 'blastn', etc.
+ self.version = version # '2.1.2' or '2.0a19MP-WashU'
+ self.description = description # '[05-Feb-1998] [Build dec ...1998]'
+
+# Query= YAL001C YAL001C, Chr I from 147596 to 147665, and 147756 to 151168,
+# reverse complement
+# (3483 letters)
+class Query:
+ def __init__(self, name, accession, description, length):
+ self.name = name # 'YAL001C'
+ self.accession = accession # or None if missing
+ self.description = description # 'YAL001C, Chr I from 147596 to ... '
+ self.length = length # 3483
+
+# Database: ArabidopsisN
+# 66,211 sequences; 69,074,155 total letters.
+class Database:
+ def __init__(self, name, letters, entries):
+ self.name = name # ArabidopsisN
+ self.letters = letters # 69074155
+ self.entries = entries # 66211
+
+class TableInfo:
+ def __init__(self, full_description, info):
+ self.__dict__.update(info)
+ self.full_description = full_description
+
+
+class Search:
+ def __init__(self, algorithm, query, database, table, hits,
+ parameters, statistics):
+ self.algorithm = algorithm
+ self.query = query
+ self.database = database
+ self.table = table
+ self.hits = hits
+ self.parameters = parameters
+ self.statistics = statistics
+
+class Hit:
+ def __init__(self, name, description, accession, length,
+ algorithm, hsps = None):
+ self.name = name
+ self.description = description
+ self.accession = accession
+ self.length = length
+ self.algorithm = algorithm
+ if hsps is None:
+ hsps = []
+ self.hsps = hsps
+
+ def __len__(self):
+ return self.length
+
+
+
+# >GB_PL:ATF18F4 AL021637 Arabidopsis thaliana DNA chromosome 4, BAC clone
+# F18F4 (ESSAII project). 2/98
+# Length = 93,646
+#
+# Minus Strand HSPs:
+#
+# Score = 226 (33.9 bits), Expect = 0.80, P = 0.55
+# Identities = 98/142 (69%), Positives = 98/142 (69%), Strand = Minus / Plus
+# [...lines deleted...]
+# Query: 2486 ATATCAAGCAATTTGATAAGATCTAG 2461
+# A AT A C ATT GA AAGATC AG
+# Sbjct: 85387 AGATTTACCTATT-GAGAAGATCAAG 85411
+
+# computed from the strings
+class _SeqLength:
+ def __init__(self, length, identical, positives, gaps):
+ self.length = length
+ self.identical = identical
+ self.positives = positives
+ self.gaps = gaps
+ def __len__(self):
+ return self.length
+ def __getattr__(self, name):
+ if name == "frac_identical":
+ return float(self.identical) / self.length
+ elif name == "frac_positives":
+ return float(self.positives) / self.length
+ raise AttributeError(name)
+
+
+class HomologySeq(_SeqLength):
+ def __init__(self, seq, identical, positives, gaps):
+ _SeqLength.__init__(self, len(seq), identical, positives, gaps)
+ self.seq = seq
+
+class HSPSeq(_SeqLength):
+ def __init__(self, name, seq, location, identical, positives, gaps):
+ _SeqLength.__init__(self, len(seq), identical, positives, gaps)
+ self.name = name
+ self.seq = seq
+ self.location = location
+
+
+class HSP(_SeqLength):
+ def __init__(self,
+ query_seq, # ATATCAAGCAATTTGATAAGATCTAG
+ homology_seq, # A AT A C ATT GA AAGATC AG
+ subject_seq, # AGATTTACCTATT-GAGAAGATCAAG
+
+ query_location, # (2486, 2461, negative strand)
+ subject_location, # (85387, 85411)
+
+ query_name, # Query (or None)
+ subject_name, # Sbjct (or None)
+
+ algorithm, # an Algorithm
+ info, # contains Key/value pairs
+ homology_gaps = None, # Is this needed?
+ ):
+ assert len(query_seq) == len(homology_seq) == len(subject_seq), \
+ (query_seq, homology_seq, subject_seq)
+ self.algorithm = algorithm
+
+ query_gaps = query_seq.count("-")
+ subject_gaps = subject_seq.count("-")
+ if homology_gaps is None:
+ homology_gaps = query_gaps + subject_gaps
+ self.info = info
+
+ identical = info["identical"]
+ # bioperl calls this 'conserved'
+ positives = info.get("positives", identical)
+
+ _SeqLength.__init__(self, len(query_seq), identical,
+ positives, homology_gaps)
+
+ self.query = HSPSeq(name = query_name,
+ seq = query_seq,
+ location = query_location,
+ identical = identical,
+ positives = positives,
+ gaps = query_gaps)
+
+ self.subject = HSPSeq(name = subject_name,
+ seq = subject_seq,
+ location = subject_location,
+ identical = identical,
+ positives = positives,
+ gaps = subject_gaps)
+ self.homology = HomologySeq(seq = homology_seq,
+ identical = identical,
+ positives = positives,
+ gaps = homology_gaps)
--- /dev/null
+# Copyright 2000-2002 Brad Chapman.
+# Copyright 2004-2005 by M de Hoon.
+# Copyright 2007-2009 by Peter Cock.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+"""Provides objects to represent biological sequences with alphabets.
+
+See also U{http://biopython.org/wiki/Seq} and the chapter in our tutorial:
+ - U{http://biopython.org/DIST/docs/tutorial/Tutorial.html}
+ - U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf}
+"""
+__docformat__ ="epytext en" #Don't just use plain text in epydoc API pages!
+
+import string #for maketrans only
+import array
+import sys
+
+#TODO - Remove this work around once we drop python 2.3 support
+try:
+ set = set
+except NameError:
+ from sets import Set as set
+
+import Alphabet
+from Alphabet import IUPAC
+from Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
+from Bio.Data import CodonTable
+
+def _maketrans(complement_mapping) :
+ """Makes a python string translation table (PRIVATE).
+
+ Arguments:
+ - complement_mapping - a dictionary such as ambiguous_dna_complement
+ and ambiguous_rna_complement from Data.IUPACData.
+
+ Returns a translation table (a string of length 256) for use with the
+ python string's translate method to use in a (reverse) complement.
+
+ Compatible with lower case and upper case sequences.
+
+ For internal use only.
+ """
+ before = ''.join(complement_mapping.keys())
+ after = ''.join(complement_mapping.values())
+ before = before + before.lower()
+ after = after + after.lower()
+ return string.maketrans(before, after)
+
+_dna_complement_table = _maketrans(ambiguous_dna_complement)
+_rna_complement_table = _maketrans(ambiguous_rna_complement)
+
+class Seq(object):
+ """A read-only sequence object (essentially a string with an alphabet).
+
+ Like normal python strings, our basic sequence object is immutable.
+ This prevents you from doing my_seq[5] = "A" for example, but does allow
+ Seq objects to be used as dictionary keys.
+
+ The Seq object provides a number of string like methods (such as count,
+ find, split and strip), which are alphabet aware where appropriate.
+
+ The Seq object also provides some biological methods, such as complement,
+ reverse_complement, transcribe, back_transcribe and translate (which are
+ not applicable to sequences with a protein alphabet).
+ """
+ def __init__(self, data, alphabet = Alphabet.generic_alphabet):
+ """Create a Seq object.
+
+ Arguments:
+ - seq - Sequence, required (string)
+ - alphabet - Optional argument, an Alphabet object from Bio.Alphabet
+
+ You will typically use Bio.SeqIO to read in sequences from files as
+ SeqRecord objects, whose sequence will be exposed as a Seq object via
+ the seq property.
+
+ However, will often want to create your own Seq objects directly:
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
+ ... IUPAC.protein)
+ >>> my_seq
+ Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
+ >>> print my_seq
+ MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
+ """
+ # Enforce string storage
+ assert (type(data) == type("") or # must use a string
+ type(data) == type(u"")) # but can be a unicode string
+ self._data = data
+ self.alphabet = alphabet # Seq API requirement
+
+ # A data property is/was a Seq API requirement
+ def _set_data(self, value) :
+ #TODO - In the next release, actually raise an exception?
+ #The Seq object is like a python string, it should be read only!
+ import warnings
+ warnings.warn("Writing to the Seq object's .data propery is deprecated.",
+ DeprecationWarning)
+ self._data = value
+ data = property(fget= lambda self : str(self),
+ fset=_set_data,
+ doc="Sequence as a string (DEPRECATED)")
+
+ def __repr__(self):
+ """Returns a (truncated) representation of the sequence for debugging."""
+ if len(self) > 60 :
+ #Shows the last three letters as it is often useful to see if there
+ #is a stop codon at the end of a sequence.
+ #Note total length is 54+3+3=60
+ return "%s('%s...%s', %s)" % (self.__class__.__name__,
+ str(self)[:54], str(self)[-3:],
+ repr(self.alphabet))
+ else :
+ return "%s(%s, %s)" % (self.__class__.__name__,
+ repr(self.data),
+ repr(self.alphabet))
+ def __str__(self):
+ """Returns the full sequence as a python string.
+
+ Note that Biopython 1.44 and earlier would give a truncated
+ version of repr(my_seq) for str(my_seq). If you are writing code
+ which need to be backwards compatible with old Biopython, you
+ should continue to use my_seq.tostring() rather than str(my_seq).
+ """
+ return self._data
+
+ """
+ TODO - Work out why this breaks test_Restriction.py
+ (Comparing Seq objects would be nice to have. May need to think about
+ hashes and the in operator for when have list/dictionary of Seq objects...)
+ def __cmp__(self, other):
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ return cmp(str(self), str(other))
+ elif isinstance(other, basestring) :
+ return cmp(str(self), other)
+ else :
+ raise TypeError
+ """
+
+ def __len__(self): return len(self._data) # Seq API requirement
+
+ def __getitem__(self, index) : # Seq API requirement
+ #Note since Python 2.0, __getslice__ is deprecated
+ #and __getitem__ is used instead.
+ #See http://docs.python.org/ref/sequence-methods.html
+ if isinstance(index, int) :
+ #Return a single letter as a string
+ return self._data[index]
+ else :
+ #Return the (sub)sequence as another Seq object
+ return Seq(self._data[index], self.alphabet)
+
+ def __add__(self, other):
+ """Add another sequence or string to this sequence."""
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
+ return self.__class__(str(self) + str(other), a)
+ elif isinstance(other, basestring) :
+ #other is a plain string - use the current alphabet
+ return self.__class__(str(self) + other, self.alphabet)
+ else :
+ raise TypeError
+
+ def __radd__(self, other):
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
+ return self.__class__(str(other) + str(self), a)
+ elif isinstance(other, basestring) :
+ #other is a plain string - use the current alphabet
+ return self.__class__(other + str(self), self.alphabet)
+ else :
+ raise TypeError
+
+ def tostring(self): # Seq API requirement
+ """Returns the full sequence as a python string.
+
+ Although not formally deprecated, you are now encouraged to use
+ str(my_seq) instead of my_seq.tostring()."""
+ return str(self)
+
+ def tomutable(self): # Needed? Or use a function?
+ """Returns the full sequence as a MutableSeq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL",
+ ... IUPAC.protein)
+ >>> my_seq
+ Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
+ >>> my_seq.tomutable()
+ MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
+
+ Note that the alphabet is preserved.
+ """
+ return MutableSeq(str(self), self.alphabet)
+
+ def _get_seq_str_and_check_alphabet(self, other_sequence) :
+ """string/Seq/MutableSeq to string, checking alphabet (PRIVATE).
+
+ For a string argument, returns the string.
+
+ For a Seq or MutableSeq, it checks the alphabet is compatible
+ (raising an exception if it isn't), and then returns a string.
+ """
+ try :
+ other_alpha = other_sequence.alphabet
+ except AttributeError :
+ #Assume other_sequence is a string
+ return other_sequence
+
+ #Other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet, other_alpha]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other_alpha)))
+ #Return as a string
+ return str(other_sequence)
+
+ def count(self, sub, start=0, end=sys.maxint):
+ """Non-overlapping count method, like that of a python string.
+
+ This behaves like the python string method of the same name,
+ which does a non-overlapping count!
+
+ Returns an integer, the number of occurrences of substring
+ argument sub in the (sub)sequence given by [start:end].
+ Optional arguments start and end are interpreted as in slice
+ notation.
+
+ Arguments:
+ - sub - a string or another Seq object to look for
+ - start - optional integer, slice start
+ - end - optional integer, slice end
+
+ e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> my_seq = Seq("AAAATGA")
+ >>> print my_seq.count("A")
+ 5
+ >>> print my_seq.count("ATG")
+ 1
+ >>> print my_seq.count(Seq("AT"))
+ 1
+ >>> print my_seq.count("AT", 2, -1)
+ 1
+
+ HOWEVER, please note because python strings and Seq objects (and
+ MutableSeq objects) do a non-overlapping search, this may not give
+ the answer you expect:
+
+ >>> "AAAA".count("AA")
+ 2
+ >>> print Seq("AAAA").count("AA")
+ 2
+
+ A non-overlapping search would give the answer as three!
+ """
+ #If it has one, check the alphabet:
+ sub_str = self._get_seq_str_and_check_alphabet(sub)
+ return str(self).count(sub_str, start, end)
+
+ def find(self, sub, start=0, end=sys.maxint):
+ """Find method, like that of a python string.
+
+ This behaves like the python string method of the same name.
+
+ Returns an integer, the index of the first occurrence of substring
+ argument sub in the (sub)sequence given by [start:end].
+
+ Arguments:
+ - sub - a string or another Seq object to look for
+ - start - optional integer, slice start
+ - end - optional integer, slice end
+
+ Returns -1 if the subsequence is NOT found.
+
+ e.g. Locating the first typical start codon, AUG, in an RNA sequence:
+
+ >>> from Bio.Seq import Seq
+ >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
+ >>> my_rna.find("AUG")
+ 3
+ """
+ #If it has one, check the alphabet:
+ sub_str = self._get_seq_str_and_check_alphabet(sub)
+ return str(self).find(sub_str, start, end)
+
+ def rfind(self, sub, start=0, end=sys.maxint):
+ """Find from right method, like that of a python string.
+
+ This behaves like the python string method of the same name.
+
+ Returns an integer, the index of the last (right most) occurrence of
+ substring argument sub in the (sub)sequence given by [start:end].
+
+ Arguments:
+ - sub - a string or another Seq object to look for
+ - start - optional integer, slice start
+ - end - optional integer, slice end
+
+ Returns -1 if the subsequence is NOT found.
+
+ e.g. Locating the last typical start codon, AUG, in an RNA sequence:
+
+ >>> from Bio.Seq import Seq
+ >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
+ >>> my_rna.rfind("AUG")
+ 15
+ """
+ #If it has one, check the alphabet:
+ sub_str = self._get_seq_str_and_check_alphabet(sub)
+ return str(self).rfind(sub_str, start, end)
+
+ def startswith(self, prefix, start=0, end=sys.maxint) :
+ """Does the Seq start with the given prefix? Returns True/False.
+
+ This behaves like the python string method of the same name.
+
+ Return True if the sequence starts with the specified prefix
+ (a string or another Seq object), False otherwise.
+ With optional start, test sequence beginning at that position.
+ With optional end, stop comparing sequence at that position.
+ prefix can also be a tuple of strings to try. e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
+ >>> my_rna.startswith("GUC")
+ True
+ >>> my_rna.startswith("AUG")
+ False
+ >>> my_rna.startswith("AUG", 3)
+ True
+ >>> my_rna.startswith(("UCC","UCA","UCG"),1)
+ True
+ """
+ #If it has one, check the alphabet:
+ if isinstance(prefix, tuple) :
+ #TODO - Once we drop support for Python 2.4, instead of this
+ #loop offload to the string method (requires Python 2.5+).
+ #Check all the alphabets first...
+ prefix_strings = [self._get_seq_str_and_check_alphabet(p) \
+ for p in prefix]
+ for prefix_str in prefix_strings :
+ if str(self).startswith(prefix_str, start, end) :
+ return True
+ return False
+ else :
+ prefix_str = self._get_seq_str_and_check_alphabet(prefix)
+ return str(self).startswith(prefix_str, start, end)
+
+ def endswith(self, suffix, start=0, end=sys.maxint) :
+ """Does the Seq end with the given suffix? Returns True/False.
+
+ This behaves like the python string method of the same name.
+
+ Return True if the sequence ends with the specified suffix
+ (a string or another Seq object), False otherwise.
+ With optional start, test sequence beginning at that position.
+ With optional end, stop comparing sequence at that position.
+ suffix can also be a tuple of strings to try. e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
+ >>> my_rna.endswith("UUG")
+ True
+ >>> my_rna.endswith("AUG")
+ False
+ >>> my_rna.endswith("AUG", 0, 18)
+ True
+ >>> my_rna.endswith(("UCC","UCA","UUG"))
+ True
+ """
+ #If it has one, check the alphabet:
+ if isinstance(suffix, tuple) :
+ #TODO - Once we drop support for Python 2.4, instead of this
+ #loop offload to the string method (requires Python 2.5+).
+ #Check all the alphabets first...
+ suffix_strings = [self._get_seq_str_and_check_alphabet(p) \
+ for p in suffix]
+ for suffix_str in suffix_strings :
+ if str(self).endswith(suffix_str, start, end) :
+ return True
+ return False
+ else :
+ suffix_str = self._get_seq_str_and_check_alphabet(suffix)
+ return str(self).endswith(suffix_str, start, end)
+
+
+ def split(self, sep=None, maxsplit=-1) :
+ """Split method, like that of a python string.
+
+ This behaves like the python string method of the same name.
+
+ Return a list of the 'words' in the string (as Seq objects),
+ using sep as the delimiter string. If maxsplit is given, at
+ most maxsplit splits are done. If maxsplit is ommited, all
+ splits are made.
+
+ Following the python string method, sep will by default be any
+ white space (tabs, spaces, newlines) but this is unlikely to
+ apply to biological sequences.
+
+ e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
+ >>> my_aa = my_rna.translate()
+ >>> my_aa
+ Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
+ >>> my_aa.split("*")
+ [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
+ >>> my_aa.split("*",1)
+ [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
+
+ See also the rsplit method:
+
+ >>> my_aa.rsplit("*",1)
+ [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
+ """
+ #If it has one, check the alphabet:
+ sep_str = self._get_seq_str_and_check_alphabet(sep)
+ #TODO - If the sep is the defined stop symbol, or gap char,
+ #should we adjust the alphabet?
+ return [Seq(part, self.alphabet) \
+ for part in str(self).split(sep_str, maxsplit)]
+
+ def rsplit(self, sep=None, maxsplit=-1) :
+ """Right split method, like that of a python string.
+
+ This behaves like the python string method of the same name.
+
+ Return a list of the 'words' in the string (as Seq objects),
+ using sep as the delimiter string. If maxsplit is given, at
+ most maxsplit splits are done COUNTING FROM THE RIGHT.
+ If maxsplit is ommited, all splits are made.
+
+ Following the python string method, sep will by default be any
+ white space (tabs, spaces, newlines) but this is unlikely to
+ apply to biological sequences.
+
+ e.g. print my_seq.rsplit("*",1)
+
+ See also the split method.
+ """
+ #If it has one, check the alphabet:
+ sep_str = self._get_seq_str_and_check_alphabet(sep)
+ try :
+ return [Seq(part, self.alphabet) \
+ for part in str(self).rsplit(sep_str, maxsplit)]
+ except AttributeError :
+ #Python 2.3 doesn't have a string rsplit method, which we can
+ #word around by reversing the sequence, using (left) split,
+ #and then reversing the answer. Not very efficient!
+ words = [Seq(word[::-1], self.alphabet) for word \
+ in str(self)[::-1].split(sep_str[::-1], maxsplit)]
+ words.reverse()
+ return words
+
+ def strip(self, chars=None) :
+ """Returns a new Seq object with leading and trailing ends stripped.
+
+ This behaves like the python string method of the same name.
+
+ Optional argument chars defines which characters to remove. If
+ ommitted or None (default) then as for the python string method,
+ this defaults to removing any white space.
+
+ e.g. print my_seq.strip("-")
+
+ See also the lstrip and rstrip methods.
+ """
+ #If it has one, check the alphabet:
+ strip_str = self._get_seq_str_and_check_alphabet(chars)
+ return Seq(str(self).strip(strip_str), self.alphabet)
+
+ def lstrip(self, chars=None) :
+ """Returns a new Seq object with leading (left) end stripped.
+
+ This behaves like the python string method of the same name.
+
+ Optional argument chars defines which characters to remove. If
+ ommitted or None (default) then as for the python string method,
+ this defaults to removing any white space.
+
+ e.g. print my_seq.lstrip("-")
+
+ See also the strip and rstrip methods.
+ """
+ #If it has one, check the alphabet:
+ strip_str = self._get_seq_str_and_check_alphabet(chars)
+ return Seq(str(self).lstrip(strip_str), self.alphabet)
+
+ def rstrip(self, chars=None) :
+ """Returns a new Seq object with trailing (right) end stripped.
+
+ This behaves like the python string method of the same name.
+
+ Optional argument chars defines which characters to remove. If
+ ommitted or None (default) then as for the python string method,
+ this defaults to removing any white space.
+
+ e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):
+
+ >>> from Bio.Alphabet import IUPAC
+ >>> from Bio.Seq import Seq
+ >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna)
+ >>> my_seq
+ Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA())
+ >>> my_seq.rstrip("A")
+ Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA())
+
+ See also the strip and lstrip methods.
+ """
+ #If it has one, check the alphabet:
+ strip_str = self._get_seq_str_and_check_alphabet(chars)
+ return Seq(str(self).rstrip(strip_str), self.alphabet)
+
+ def complement(self):
+ """Returns the complement sequence. New Seq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
+ >>> my_dna
+ Seq('CCCCCGATAG', IUPACUnambiguousDNA())
+ >>> my_dna.complement()
+ Seq('GGGGGCTATC', IUPACUnambiguousDNA())
+
+ You can of course used mixed case sequences,
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import generic_dna
+ >>> my_dna = Seq("CCCCCgatA-GD", generic_dna)
+ >>> my_dna
+ Seq('CCCCCgatA-GD', DNAAlphabet())
+ >>> my_dna.complement()
+ Seq('GGGGGctaT-CH', DNAAlphabet())
+
+ Note in the above example, ambiguous character D denotes
+ G, A or T so its complement is H (for C, T or A).
+
+ Trying to complement a protein sequence raises an exception.
+
+ >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
+ >>> my_protein.complement()
+ Traceback (most recent call last):
+ ...
+ ValueError: Proteins do not have complements!
+ """
+ base = Alphabet._get_base_alphabet(self.alphabet)
+ if isinstance(base, Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins do not have complements!")
+ if isinstance(base, Alphabet.DNAAlphabet) :
+ ttable = _dna_complement_table
+ elif isinstance(base, Alphabet.RNAAlphabet) :
+ ttable = _rna_complement_table
+ elif ('U' in self._data or 'u' in self._data) \
+ and ('T' in self._data or 't' in self._data):
+ #TODO - Handle this cleanly?
+ raise ValueError("Mixed RNA/DNA found")
+ elif 'U' in self._data or 'u' in self._data:
+ ttable = _rna_complement_table
+ else:
+ ttable = _dna_complement_table
+ #Much faster on really long sequences than the previous loop based one.
+ #thx to Michael Palmer, University of Waterloo
+ return Seq(str(self).translate(ttable), self.alphabet)
+
+ def reverse_complement(self):
+ """Returns the reverse complement sequence. New Seq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
+ >>> my_dna
+ Seq('CCCCCGATAGNR', IUPACAmbiguousDNA())
+ >>> my_dna.reverse_complement()
+ Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())
+
+ Note in the above example, since R = G or A, its complement
+ is Y (which denotes C or T).
+
+ You can of course used mixed case sequences,
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import generic_dna
+ >>> my_dna = Seq("CCCCCgatA-G", generic_dna)
+ >>> my_dna
+ Seq('CCCCCgatA-G', DNAAlphabet())
+ >>> my_dna.reverse_complement()
+ Seq('C-TatcGGGGG', DNAAlphabet())
+
+ Trying to complement a protein sequence raises an exception:
+
+ >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
+ >>> my_protein.reverse_complement()
+ Traceback (most recent call last):
+ ...
+ ValueError: Proteins do not have complements!
+ """
+ #Use -1 stride/step to reverse the complement
+ return self.complement()[::-1]
+
+ def transcribe(self):
+ """Returns the RNA sequence from a DNA sequence. New Seq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
+ ... IUPAC.unambiguous_dna)
+ >>> coding_dna
+ Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
+ >>> coding_dna.transcribe()
+ Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
+
+ Trying to transcribe a protein or RNA sequence raises an exception:
+
+ >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
+ >>> my_protein.transcribe()
+ Traceback (most recent call last):
+ ...
+ ValueError: Proteins cannot be transcribed!
+ """
+ base = Alphabet._get_base_alphabet(self.alphabet)
+ if isinstance(base, Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins cannot be transcribed!")
+ if isinstance(base, Alphabet.RNAAlphabet) :
+ raise ValueError("RNA cannot be transcribed!")
+
+ if self.alphabet==IUPAC.unambiguous_dna:
+ alphabet = IUPAC.unambiguous_rna
+ elif self.alphabet==IUPAC.ambiguous_dna:
+ alphabet = IUPAC.ambiguous_rna
+ else:
+ alphabet = Alphabet.generic_rna
+ return Seq(str(self).replace('T','U').replace('t','u'), alphabet)
+
+ def back_transcribe(self):
+ """Returns the DNA sequence from an RNA sequence. New Seq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
+ ... IUPAC.unambiguous_rna)
+ >>> messenger_rna
+ Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
+ >>> messenger_rna.back_transcribe()
+ Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
+
+ Trying to back-transcribe a protein or DNA sequence raises an
+ exception:
+
+ >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
+ >>> my_protein.back_transcribe()
+ Traceback (most recent call last):
+ ...
+ ValueError: Proteins cannot be back transcribed!
+ """
+ base = Alphabet._get_base_alphabet(self.alphabet)
+ if isinstance(base, Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins cannot be back transcribed!")
+ if isinstance(base, Alphabet.DNAAlphabet) :
+ raise ValueError("DNA cannot be back transcribed!")
+
+ if self.alphabet==IUPAC.unambiguous_rna:
+ alphabet = IUPAC.unambiguous_dna
+ elif self.alphabet==IUPAC.ambiguous_rna:
+ alphabet = IUPAC.ambiguous_dna
+ else:
+ alphabet = Alphabet.generic_dna
+ return Seq(str(self).replace("U", "T").replace("u", "t"), alphabet)
+
+ def translate(self, table="Standard", stop_symbol="*", to_stop=False):
+ """Turns a nucleotide sequence into a protein sequence. New Seq object.
+
+ This method will translate DNA or RNA sequences, and those with a
+ nucleotide or generic alphabet. Trying to translate a protein
+ sequence raises an exception.
+
+ Arguments:
+ - table - Which codon table to use? This can be either a name
+ (string) or an NCBI identifier (integer). This defaults
+ to the "Standard" table.
+ - stop_symbol - Single character string, what to use for terminators.
+ This defaults to the asterisk, "*".
+ - to_stop - Boolean, defaults to False meaning do a full translation
+ continuing on past any stop codons (translated as the
+ specified stop_symbol). If True, translation is
+ terminated at the first in frame stop codon (and the
+ stop_symbol is not appended to the returned protein
+ sequence).
+
+ e.g. Using the standard table:
+
+ >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
+ >>> coding_dna.translate()
+ Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
+ >>> coding_dna.translate(stop_symbol="@")
+ Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
+ >>> coding_dna.translate(to_stop=True)
+ Seq('VAIVMGR', ExtendedIUPACProtein())
+
+ Now using NCBI table 2, where TGA is not a stop codon:
+
+ >>> coding_dna.translate(table=2)
+ Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
+ >>> coding_dna.translate(table=2, to_stop=True)
+ Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())
+
+ If the sequence has no in-frame stop codon, then the to_stop argument
+ has no effect:
+
+ >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
+ >>> coding_dna2.translate()
+ Seq('LAIVMGR', ExtendedIUPACProtein())
+ >>> coding_dna2.translate(to_stop=True)
+ Seq('LAIVMGR', ExtendedIUPACProtein())
+
+ NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
+ or a stop codon. These are translated as "X". Any invalid codon
+ (e.g. "TA?" or "T-A") will throw a TranslationError.
+
+ NOTE - Does NOT support gapped sequences.
+
+ NOTE - This does NOT behave like the python string's translate
+ method. For that use str(my_seq).translate(...) instead.
+ """
+ try:
+ table_id = int(table)
+ except ValueError:
+ table_id = None
+ if isinstance(table, str) and len(table)==256 :
+ raise ValueError("The Seq object translate method DOES NOT take " \
+ + "a 256 character string mapping table like " \
+ + "the python string object's translate method. " \
+ + "Use str(my_seq).translate(...) instead.")
+ if isinstance(Alphabet._get_base_alphabet(self.alphabet),
+ Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins cannot be translated!")
+ if self.alphabet==IUPAC.unambiguous_dna:
+ #Will use standard IUPAC protein alphabet, no need for X
+ if table_id is None:
+ codon_table = CodonTable.unambiguous_dna_by_name[table]
+ else:
+ codon_table = CodonTable.unambiguous_dna_by_id[table_id]
+ #elif self.alphabet==IUPAC.ambiguous_dna:
+ # if table_id is None:
+ # codon_table = CodonTable.ambiguous_dna_by_name[table]
+ # else:
+ # codon_table = CodonTable.ambiguous_dna_by_id[table_id]
+ elif self.alphabet==IUPAC.unambiguous_rna:
+ #Will use standard IUPAC protein alphabet, no need for X
+ if table_id is None:
+ codon_table = CodonTable.unambiguous_rna_by_name[table]
+ else:
+ codon_table = CodonTable.unambiguous_rna_by_id[table_id]
+ #elif self.alphabet==IUPAC.ambiguous_rna:
+ # if table_id is None:
+ # codon_table = CodonTable.ambiguous_rna_by_name[table]
+ # else:
+ # codon_table = CodonTable.ambiguous_rna_by_id[table_id]
+ else:
+ #This will use the extend IUPAC protein alphabet with X etc.
+ #The same table can be used for RNA or DNA (we use this for
+ #translating strings).
+ if table_id is None:
+ codon_table = CodonTable.ambiguous_generic_by_name[table]
+ else:
+ codon_table = CodonTable.ambiguous_generic_by_id[table_id]
+ protein = _translate_str(str(self), codon_table, stop_symbol, to_stop)
+ if stop_symbol in protein :
+ alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
+ stop_symbol = stop_symbol)
+ else :
+ alphabet = codon_table.protein_alphabet
+ return Seq(protein, alphabet)
+
+class UnknownSeq(Seq):
+ """A read-only sequence object of known length but unknown contents.
+
+ If you have an unknown sequence, you can represent this with a normal
+ Seq object, for example:
+
+ >>> my_seq = Seq("N"*5)
+ >>> my_seq
+ Seq('NNNNN', Alphabet())
+ >>> len(my_seq)
+ 5
+ >>> print my_seq
+ NNNNN
+
+ However, this is rather wasteful of memory (especially for large
+ sequences), which is where this class is most usefull:
+
+ >>> unk_five = UnknownSeq(5)
+ >>> unk_five
+ UnknownSeq(5, alphabet = Alphabet(), character = '?')
+ >>> len(unk_five)
+ 5
+ >>> print(unk_five)
+ ?????
+
+ You can add unknown sequence together, provided their alphabets and
+ characters are compatible, and get another memory saving UnknownSeq:
+
+ >>> unk_four = UnknownSeq(4)
+ >>> unk_four
+ UnknownSeq(4, alphabet = Alphabet(), character = '?')
+ >>> unk_four + unk_five
+ UnknownSeq(9, alphabet = Alphabet(), character = '?')
+
+ If the alphabet or characters don't match up, the addition gives an
+ ordinary Seq object:
+
+ >>> unk_nnnn = UnknownSeq(4, character = "N")
+ >>> unk_nnnn
+ UnknownSeq(4, alphabet = Alphabet(), character = 'N')
+ >>> unk_nnnn + unk_four
+ Seq('NNNN????', Alphabet())
+
+ Combining with a real Seq gives a new Seq object:
+
+ >>> known_seq = Seq("ACGT")
+ >>> unk_four + known_seq
+ Seq('????ACGT', Alphabet())
+ >>> known_seq + unk_four
+ Seq('ACGT????', Alphabet())
+ """
+ def __init__(self, length, alphabet = Alphabet.generic_alphabet, character = None) :
+ """Create a new UnknownSeq object.
+
+ If character is ommited, it is determed from the alphabet, "N" for
+ nucleotides, "X" for proteins, and "?" otherwise.
+ """
+ self._length = int(length)
+ if self._length < 0 :
+ #TODO - Block zero length UnknownSeq? You can just use a Seq!
+ raise ValueError("Length must not be negative.")
+ self.alphabet = alphabet
+ if character :
+ if len(character) != 1 :
+ raise ValueError("character argument should be a single letter string.")
+ self._character = character
+ else :
+ base = Alphabet._get_base_alphabet(alphabet)
+ #TODO? Check the case of the letters in the alphabet?
+ #We may have to use "n" instead of "N" etc.
+ if isinstance(base, Alphabet.NucleotideAlphabet) :
+ self._character = "N"
+ elif isinstance(base, Alphabet.ProteinAlphabet) :
+ self._character = "X"
+ else :
+ self._character = "?"
+
+ def __len__(self) :
+ """Returns the stated length of the unknown sequence."""
+ return self._length
+
+ def __str__(self) :
+ """Returns the unknown sequence as full string of the given length."""
+ return self._character * self._length
+
+ def __repr__(self):
+ return "UnknownSeq(%i, alphabet = %s, character = %s)" \
+ % (self._length, repr(self.alphabet), repr(self._character))
+
+ def __add__(self, other) :
+ if isinstance(other, UnknownSeq) \
+ and other._character == self._character :
+ #TODO - Check the alphabets match
+ return UnknownSeq(len(self)+len(other),
+ self.alphabet, self._character)
+ #Offload to the base class...
+ return Seq(str(self), self.alphabet) + other
+
+ def __radd__(self, other) :
+ if isinstance(other, UnknownSeq) \
+ and other._character == self._character :
+ #TODO - Check the alphabets match
+ return UnknownSeq(len(self)+len(other),
+ self.alphabet, self._character)
+ #Offload to the base class...
+ return other + Seq(str(self), self.alphabet)
+
+ def __getitem__(self, index):
+ if isinstance(index, int) :
+ #TODO - Check the bounds without wasting memory
+ return str(self)[index]
+ else :
+ #TODO - Work out the length without wasting memory
+ return UnknownSeq(len(("#"*self._length)[index]),
+ self.alphabet, self._character)
+
+ def count(self, sub, start=0, end=sys.maxint):
+ """Non-overlapping count method, like that of a python string.
+
+ This behaves like the python string (and Seq object) method of the
+ same name, which does a non-overlapping count!
+
+ Returns an integer, the number of occurrences of substring
+ argument sub in the (sub)sequence given by [start:end].
+ Optional arguments start and end are interpreted as in slice
+ notation.
+
+ Arguments:
+ - sub - a string or another Seq object to look for
+ - start - optional integer, slice start
+ - end - optional integer, slice end
+
+ >>> "NNNN".count("N")
+ 4
+ >>> Seq("NNNN").count("N")
+ 4
+ >>> UnknownSeq(4, character="N").count("N")
+ 4
+ >>> UnknownSeq(4, character="N").count("A")
+ 0
+ >>> UnknownSeq(4, character="N").count("AA")
+ 0
+
+ HOWEVER, please note because that python strings and Seq objects (and
+ MutableSeq objects) do a non-overlapping search, this may not give
+ the answer you expect:
+
+ >>> UnknownSeq(4, character="N").count("NN")
+ 2
+ >>> UnknownSeq(4, character="N").count("NNN")
+ 1
+ """
+ sub_str = self._get_seq_str_and_check_alphabet(sub)
+ if len(sub_str) == 1 :
+ if str(sub_str) == self._character :
+ if start==0 and end >= self._length :
+ return self._length
+ else :
+ #This could be done more cleverly...
+ return str(self).count(sub_str, start, end)
+ else :
+ return 0
+ else :
+ if set(sub_str) == set(self._character) :
+ if start==0 and end >= self._length :
+ return self._length // len(sub_str)
+ else :
+ #This could be done more cleverly...
+ return str(self).count(sub_str, start, end)
+ else :
+ return 0
+
+ def complement(self) :
+ """The complement of an unknown nucleotide equals itself.
+
+ >>> my_nuc = UnknownSeq(8)
+ >>> my_nuc
+ UnknownSeq(8, alphabet = Alphabet(), character = '?')
+ >>> print my_nuc
+ ????????
+ >>> my_nuc.complement()
+ UnknownSeq(8, alphabet = Alphabet(), character = '?')
+ >>> print my_nuc.complement()
+ ????????
+ """
+ if isinstance(Alphabet._get_base_alphabet(self.alphabet),
+ Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins do not have complements!")
+ return self
+
+ def reverse_complement(self) :
+ """The reverse complement of an unknown nucleotide equals itself.
+
+ >>> my_nuc = UnknownSeq(10)
+ >>> my_nuc
+ UnknownSeq(10, alphabet = Alphabet(), character = '?')
+ >>> print my_nuc
+ ??????????
+ >>> my_nuc.reverse_complement()
+ UnknownSeq(10, alphabet = Alphabet(), character = '?')
+ >>> print my_nuc.reverse_complement()
+ ??????????
+ """
+ if isinstance(Alphabet._get_base_alphabet(self.alphabet),
+ Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins do not have complements!")
+ return self
+
+ def transcribe(self) :
+ """Returns unknown RNA sequence from an unknown DNA sequence.
+
+ >>> my_dna = UnknownSeq(10, character="N")
+ >>> my_dna
+ UnknownSeq(10, alphabet = Alphabet(), character = 'N')
+ >>> print my_dna
+ NNNNNNNNNN
+ >>> my_rna = my_dna.transcribe()
+ >>> my_rna
+ UnknownSeq(10, alphabet = RNAAlphabet(), character = 'N')
+ >>> print my_rna
+ NNNNNNNNNN
+ """
+ #Offload the alphabet stuff
+ s = Seq(self._character, self.alphabet).transcribe()
+ return UnknownSeq(self._length, s.alphabet, self._character)
+
+ def back_transcribe(self) :
+ """Returns unknown DNA sequence from an unknown RNA sequence.
+
+ >>> my_rna = UnknownSeq(20, character="N")
+ >>> my_rna
+ UnknownSeq(20, alphabet = Alphabet(), character = 'N')
+ >>> print my_rna
+ NNNNNNNNNNNNNNNNNNNN
+ >>> my_dna = my_rna.back_transcribe()
+ >>> my_dna
+ UnknownSeq(20, alphabet = DNAAlphabet(), character = 'N')
+ >>> print my_dna
+ NNNNNNNNNNNNNNNNNNNN
+ """
+ #Offload the alphabet stuff
+ s = Seq(self._character, self.alphabet).back_transcribe()
+ return UnknownSeq(self._length, s.alphabet, self._character)
+
+ def translate(self, **kwargs) :
+ """Translate an unknown nucleotide sequence into an unknown protein.
+
+ e.g.
+
+ >>> my_seq = UnknownSeq(11, character="N")
+ >>> print my_seq
+ NNNNNNNNNNN
+ >>> my_protein = my_seq.translate()
+ >>> my_protein
+ UnknownSeq(3, alphabet = ProteinAlphabet(), character = 'X')
+ >>> print my_protein
+ XXX
+
+ In comparison, using a normal Seq object:
+
+ >>> my_seq = Seq("NNNNNNNNNNN")
+ >>> print my_seq
+ NNNNNNNNNNN
+ >>> my_protein = my_seq.translate()
+ >>> my_protein
+ Seq('XXX', ExtendedIUPACProtein())
+ >>> print my_protein
+ XXX
+
+ """
+ if isinstance(Alphabet._get_base_alphabet(self.alphabet),
+ Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins cannot be translated!")
+ return UnknownSeq(self._length//3, Alphabet.generic_protein, "X")
+
+
+class MutableSeq(object):
+ """An editable sequence object (with an alphabet).
+
+ Unlike normal python strings and our basic sequence object (the Seq class)
+ which are immuatable, the MutableSeq lets you edit the sequence in place.
+ However, this means you cannot use a MutableSeq object as a dictionary key.
+
+ >>> from Bio.Seq import MutableSeq
+ >>> from Bio.Alphabet import generic_dna
+ >>> my_seq = MutableSeq("ACTCGTCGTCG", generic_dna)
+ >>> my_seq
+ MutableSeq('ACTCGTCGTCG', DNAAlphabet())
+ >>> my_seq[5]
+ 'T'
+ >>> my_seq[5] = "A"
+ >>> my_seq
+ MutableSeq('ACTCGACGTCG', DNAAlphabet())
+ >>> my_seq[5]
+ 'A'
+ >>> my_seq[5:8] = "NNN"
+ >>> my_seq
+ MutableSeq('ACTCGNNNTCG', DNAAlphabet())
+ >>> len(my_seq)
+ 11
+
+ Note that the MutableSeq object does not support as many string-like
+ or biological methods as the Seq object.
+ """
+ def __init__(self, data, alphabet = Alphabet.generic_alphabet):
+ if type(data) == type(""):
+ self.data = array.array("c", data)
+ else:
+ self.data = data # assumes the input is an array
+ self.alphabet = alphabet
+
+ def __repr__(self):
+ """Returns a (truncated) representation of the sequence for debugging."""
+ if len(self) > 60 :
+ #Shows the last three letters as it is often useful to see if there
+ #is a stop codon at the end of a sequence.
+ #Note total length is 54+3+3=60
+ return "%s('%s...%s', %s)" % (self.__class__.__name__,
+ str(self[:54]), str(self[-3:]),
+ repr(self.alphabet))
+ else :
+ return "%s('%s', %s)" % (self.__class__.__name__,
+ str(self),
+ repr(self.alphabet))
+
+ def __str__(self):
+ """Returns the full sequence as a python string.
+
+ Note that Biopython 1.44 and earlier would give a truncated
+ version of repr(my_seq) for str(my_seq). If you are writing code
+ which needs to be backwards compatible with old Biopython, you
+ should continue to use my_seq.tostring() rather than str(my_seq).
+ """
+ #See test_GAQueens.py for an historic usage of a non-string alphabet!
+ return "".join(self.data)
+
+ def __cmp__(self, other):
+ """Compare the sequence for to another sequence or a string.
+
+ If compared to another sequence the alphabets must be compatible.
+ Comparing DNA to RNA, or Nucleotide to Protein will raise an
+ exception.
+
+ Otherwise only the sequence itself is compared, not the precise
+ alphabet.
+
+ This method indirectly supports ==, < , etc."""
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ if isinstance(other, MutableSeq):
+ #See test_GAQueens.py for an historic usage of a non-string
+ #alphabet! Comparing the arrays supports this.
+ return cmp(self.data, other.data)
+ else :
+ return cmp(str(self), str(other))
+ elif isinstance(other, basestring) :
+ return cmp(str(self), other)
+ else :
+ raise TypeError
+
+ def __len__(self): return len(self.data)
+
+ def __getitem__(self, index) :
+ #Note since Python 2.0, __getslice__ is deprecated
+ #and __getitem__ is used instead.
+ #See http://docs.python.org/ref/sequence-methods.html
+ if isinstance(index, int) :
+ #Return a single letter as a string
+ return self.data[index]
+ else :
+ #Return the (sub)sequence as another Seq object
+ return MutableSeq(self.data[index], self.alphabet)
+
+ def __setitem__(self, index, value):
+ #Note since Python 2.0, __setslice__ is deprecated
+ #and __setitem__ is used instead.
+ #See http://docs.python.org/ref/sequence-methods.html
+ if isinstance(index, int) :
+ #Replacing a single letter with a new string
+ self.data[index] = value
+ else :
+ #Replacing a sub-sequence
+ if isinstance(value, MutableSeq):
+ self.data[index] = value.data
+ elif isinstance(value, type(self.data)):
+ self.data[index] = value
+ else:
+ self.data[index] = array.array("c", str(value))
+
+ def __delitem__(self, index):
+ #Note since Python 2.0, __delslice__ is deprecated
+ #and __delitem__ is used instead.
+ #See http://docs.python.org/ref/sequence-methods.html
+
+ #Could be deleting a single letter, or a slice
+ del self.data[index]
+
+ def __add__(self, other):
+ """Add another sequence or string to this sequence.
+
+ Returns a new MutableSeq object."""
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
+ if isinstance(other, MutableSeq):
+ #See test_GAQueens.py for an historic usage of a non-string
+ #alphabet! Adding the arrays should support this.
+ return self.__class__(self.data + other.data, a)
+ else :
+ return self.__class__(str(self) + str(other), a)
+ elif isinstance(other, basestring) :
+ #other is a plain string - use the current alphabet
+ return self.__class__(str(self) + str(other), self.alphabet)
+ else :
+ raise TypeError
+
+ def __radd__(self, other):
+ if hasattr(other, "alphabet") :
+ #other should be a Seq or a MutableSeq
+ if not Alphabet._check_type_compatible([self.alphabet,
+ other.alphabet]) :
+ raise TypeError("Incompatable alphabets %s and %s" \
+ % (repr(self.alphabet), repr(other.alphabet)))
+ #They should be the same sequence type (or one of them is generic)
+ a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
+ if isinstance(other, MutableSeq):
+ #See test_GAQueens.py for an historic usage of a non-string
+ #alphabet! Adding the arrays should support this.
+ return self.__class__(other.data + self.data, a)
+ else :
+ return self.__class__(str(other) + str(self), a)
+ elif isinstance(other, basestring) :
+ #other is a plain string - use the current alphabet
+ return self.__class__(str(other) + str(self), self.alphabet)
+ else :
+ raise TypeError
+
+ def append(self, c):
+ self.data.append(c)
+
+ def insert(self, i, c):
+ self.data.insert(i, c)
+
+ def pop(self, i = (-1)):
+ c = self.data[i]
+ del self.data[i]
+ return c
+
+ def remove(self, item):
+ for i in range(len(self.data)):
+ if self.data[i] == item:
+ del self.data[i]
+ return
+ raise ValueError("MutableSeq.remove(x): x not in list")
+
+ def count(self, sub, start=0, end=sys.maxint):
+ """Non-overlapping count method, like that of a python string.
+
+ This behaves like the python string method of the same name,
+ which does a non-overlapping count!
+
+ Returns an integer, the number of occurrences of substring
+ argument sub in the (sub)sequence given by [start:end].
+ Optional arguments start and end are interpreted as in slice
+ notation.
+
+ Arguments:
+ - sub - a string or another Seq object to look for
+ - start - optional integer, slice start
+ - end - optional integer, slice end
+
+ e.g.
+
+ >>> from Bio.Seq import MutableSeq
+ >>> my_mseq = MutableSeq("AAAATGA")
+ >>> print my_mseq.count("A")
+ 5
+ >>> print my_mseq.count("ATG")
+ 1
+ >>> print my_mseq.count(Seq("AT"))
+ 1
+ >>> print my_mseq.count("AT", 2, -1)
+ 1
+
+ HOWEVER, please note because that python strings, Seq objects and
+ MutableSeq objects do a non-overlapping search, this may not give
+ the answer you expect:
+
+ >>> "AAAA".count("AA")
+ 2
+ >>> print MutableSeq("AAAA").count("AA")
+ 2
+
+ A non-overlapping search would give the answer as three!
+ """
+ try :
+ #TODO - Should we check the alphabet?
+ search = sub.tostring()
+ except AttributeError :
+ search = sub
+
+ if not isinstance(search, basestring) :
+ raise TypeError("expected a string, Seq or MutableSeq")
+
+ if len(search) == 1 :
+ #Try and be efficient and work directly from the array.
+ count = 0
+ for c in self.data[start:end]:
+ if c == search: count += 1
+ return count
+ else :
+ #TODO - Can we do this more efficiently?
+ return self.tostring().count(search, start, end)
+
+ def index(self, item):
+ for i in range(len(self.data)):
+ if self.data[i] == item:
+ return i
+ raise ValueError("MutableSeq.index(x): x not in list")
+
+ def reverse(self):
+ """Modify the mutable sequence to reverse itself.
+
+ No return value.
+ """
+ self.data.reverse()
+
+ def complement(self):
+ """Modify the mutable sequence to take on its complement.
+
+ Trying to complement a protein sequence raises an exception.
+
+ No return value.
+ """
+ if isinstance(Alphabet._get_base_alphabet(self.alphabet),
+ Alphabet.ProteinAlphabet) :
+ raise ValueError("Proteins do not have complements!")
+ if self.alphabet in (IUPAC.ambiguous_dna, IUPAC.unambiguous_dna):
+ d = ambiguous_dna_complement
+ elif self.alphabet in (IUPAC.ambiguous_rna, IUPAC.unambiguous_rna):
+ d = ambiguous_rna_complement
+ elif 'U' in self.data and 'T' in self.data :
+ #TODO - Handle this cleanly?
+ raise ValueError("Mixed RNA/DNA found")
+ elif 'U' in self.data:
+ d = ambiguous_rna_complement
+ else:
+ d = ambiguous_dna_complement
+ c = dict([(x.lower(), y.lower()) for x,y in d.iteritems()])
+ d.update(c)
+ self.data = map(lambda c: d[c], self.data)
+ self.data = array.array('c', self.data)
+
+ def reverse_complement(self):
+ """Modify the mutable sequence to take on its reverse complement.
+
+ Trying to reverse complement a protein sequence raises an exception.
+
+ No return value.
+ """
+ self.complement()
+ self.data.reverse()
+
+ ## Sorting a sequence makes no sense.
+ # def sort(self, *args): self.data.sort(*args)
+
+ def extend(self, other):
+ if isinstance(other, MutableSeq):
+ for c in other.data:
+ self.data.append(c)
+ else:
+ for c in other:
+ self.data.append(c)
+
+ def tostring(self):
+ """Returns the full sequence as a python string.
+
+ Although not formally deprecated, you are now encouraged to use
+ str(my_seq) instead of my_seq.tostring().
+
+ Because str(my_seq) will give you the full sequence as a python string,
+ there is often no need to make an explicit conversion. For example,
+
+ print "ID={%s}, sequence={%s}" % (my_name, my_seq)
+
+ On Biopython 1.44 or older you would have to have done this:
+
+ print "ID={%s}, sequence={%s}" % (my_name, my_seq.tostring())
+ """
+ return "".join(self.data)
+
+ def toseq(self):
+ """Returns the full sequence as a new immutable Seq object.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.Alphabet import IUPAC
+ >>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL", \
+ IUPAC.protein)
+ >>> my_mseq
+ MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
+ >>> my_mseq.toseq()
+ Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
+
+ Note that the alphabet is preserved.
+ """
+ return Seq("".join(self.data), self.alphabet)
+
+# The transcribe, backward_transcribe, and translate functions are
+# user-friendly versions of the corresponding functions in Bio.Transcribe
+# and Bio.Translate. The functions work both on Seq objects, and on strings.
+
+def transcribe(dna):
+ """Transcribes a DNA sequence into RNA.
+
+ If given a string, returns a new string object.
+
+ Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
+
+ Trying to transcribe a protein or RNA sequence raises an exception.
+
+ e.g.
+
+ >>> transcribe("ACTGN")
+ 'ACUGN'
+ """
+ if isinstance(dna, Seq) :
+ return dna.transcribe()
+ elif isinstance(dna, MutableSeq):
+ return dna.toseq().transcribe()
+ else:
+ return dna.replace('T','U').replace('t','u')
+
+def back_transcribe(rna):
+ """Back-transcribes an RNA sequence into DNA.
+
+ If given a string, returns a new string object.
+
+ Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
+
+ Trying to transcribe a protein or DNA sequence raises an exception.
+
+ e.g.
+
+ >>> back_transcribe("ACUGN")
+ 'ACTGN'
+ """
+ if isinstance(rna, Seq) :
+ return rna.back_transcribe()
+ elif isinstance(rna, MutableSeq):
+ return rna.toseq().back_transcribe()
+ else:
+ return rna.replace('U','T').replace('u','t')
+
+def _translate_str(sequence, table, stop_symbol="*",
+ to_stop=False, pos_stop="X") :
+ """Helper function to translate a nucleotide string (PRIVATE).
+
+ Arguments:
+ - sequence - a string
+ - table - a CodonTable object (NOT a table name or id number)
+ - stop_symbol - a single character string, what to use for terminators.
+ - to_stop - boolean, should translation terminate at the first
+ in frame stop codon? If there is no in-frame stop codon
+ then translation continues to the end.
+ - pos_stop - a single character string for a possible stop codon
+ (e.g. TAN or NNN)
+
+ Returns a string.
+
+ e.g.
+
+ >>> from Bio.Data import CodonTable
+ >>> table = CodonTable.ambiguous_dna_by_id[1]
+ >>> _translate_str("AAA", table)
+ 'K'
+ >>> _translate_str("TAR", table)
+ '*'
+ >>> _translate_str("TAN", table)
+ 'X'
+ >>> _translate_str("TAN", table, pos_stop="@")
+ '@'
+ >>> _translate_str("TA?", table)
+ Traceback (most recent call last):
+ ...
+ TranslationError: Codon 'TA?' is invalid
+ """
+ sequence = sequence.upper()
+ amino_acids = []
+ forward_table = table.forward_table
+ stop_codons = table.stop_codons
+ if table.nucleotide_alphabet.letters is not None :
+ valid_letters = set(table.nucleotide_alphabet.letters.upper())
+ else :
+ #Assume the worst case, ambiguous DNA or RNA:
+ valid_letters = set(IUPAC.ambiguous_dna.letters.upper() + \
+ IUPAC.ambiguous_rna.letters.upper())
+
+ n = len(sequence)
+ for i in xrange(0,n-n%3,3) :
+ codon = sequence[i:i+3]
+ try :
+ amino_acids.append(forward_table[codon])
+ except (KeyError, CodonTable.TranslationError) :
+ #Todo? Treat "---" as a special case (gapped translation)
+ if codon in table.stop_codons :
+ if to_stop : break
+ amino_acids.append(stop_symbol)
+ elif valid_letters.issuperset(set(codon)) :
+ #Possible stop codon (e.g. NNN or TAN)
+ amino_acids.append(pos_stop)
+ else :
+ raise CodonTable.TranslationError(\
+ "Codon '%s' is invalid" % codon)
+ return "".join(amino_acids)
+
+def translate(sequence, table="Standard", stop_symbol="*", to_stop=False):
+ """Translate a nucleotide sequence into amino acids.
+
+ If given a string, returns a new string object. Given a Seq or
+ MutableSeq, returns a Seq object with a protein alphabet.
+
+ Arguments:
+ - table - Which codon table to use? This can be either a name
+ (string) or an NCBI identifier (integer). Defaults
+ to the "Standard" table.
+ - stop_symbol - Single character string, what to use for any
+ terminators, defaults to the asterisk, "*".
+ - to_stop - Boolean, defaults to False meaning do a full
+ translation continuing on past any stop codons
+ (translated as the specified stop_symbol). If
+ True, translation is terminated at the first in
+ frame stop codon (and the stop_symbol is not
+ appended to the returned protein sequence).
+
+ A simple string example using the default (standard) genetic code:
+
+ >>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
+ >>> translate(coding_dna)
+ 'VAIVMGR*KGAR*'
+ >>> translate(coding_dna, stop_symbol="@")
+ 'VAIVMGR@KGAR@'
+ >>> translate(coding_dna, to_stop=True)
+ 'VAIVMGR'
+
+ Now using NCBI table 2, where TGA is not a stop codon:
+
+ >>> translate(coding_dna, table=2)
+ 'VAIVMGRWKGAR*'
+ >>> translate(coding_dna, table=2, to_stop=True)
+ 'VAIVMGRWKGAR'
+
+ Note that if the sequence has no in-frame stop codon, then the to_stop
+ argument has no effect:
+
+ >>> coding_dna2 = "GTGGCCATTGTAATGGGCCGC"
+ >>> translate(coding_dna2)
+ 'VAIVMGR'
+ >>> translate(coding_dna2, to_stop=True)
+ 'VAIVMGR'
+
+ NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
+ or a stop codon. These are translated as "X". Any invalid codon
+ (e.g. "TA?" or "T-A") will throw a TranslationError.
+
+ NOTE - Does NOT support gapped sequences.
+
+ It will however translate either DNA or RNA.
+ """
+ if isinstance(sequence, Seq) :
+ return sequence.translate(table, stop_symbol, to_stop)
+ elif isinstance(sequence, MutableSeq):
+ #Return a Seq object
+ return sequence.toseq().translate(table, stop_symbol, to_stop)
+ else:
+ #Assume its a string, return a string
+ try :
+ codon_table = CodonTable.ambiguous_generic_by_id[int(table)]
+ except ValueError :
+ codon_table = CodonTable.ambiguous_generic_by_name[table]
+ return _translate_str(sequence, codon_table, stop_symbol, to_stop)
+
+def reverse_complement(sequence):
+ """Returns the reverse complement sequence of a nucleotide string.
+
+ If given a string, returns a new string object.
+ Given a Seq or a MutableSeq, returns a new Seq object with the same alphabet.
+
+ Supports unambiguous and ambiguous nucleotide sequences.
+
+ e.g.
+
+ >>> reverse_complement("ACTG-NH")
+ 'DN-CAGT'
+ """
+ if isinstance(sequence, Seq) :
+ #Return a Seq
+ return sequence.reverse_complement()
+ elif isinstance(sequence, MutableSeq) :
+ #Return a Seq
+ #Don't use the MutableSeq reverse_complement method as it is 'in place'.
+ return sequence.toseq().reverse_complement()
+
+ #Assume its a string.
+ #In order to avoid some code duplication, the old code would turn the string
+ #into a Seq, use the reverse_complement method, and convert back to a string.
+ #This worked, but is over five times slower on short sequences!
+ if ('U' in sequence or 'u' in sequence) \
+ and ('T' in sequence or 't' in sequence):
+ raise ValueError("Mixed RNA/DNA found")
+ elif 'U' in sequence or 'u' in sequence:
+ ttable = _rna_complement_table
+ else:
+ ttable = _dna_complement_table
+ return sequence.translate(ttable)[::-1]
+
+def _test():
+ """Run the Bio.Seq module's doctests."""
+ print "Runing doctests..."
+ import doctest
+ doctest.testmod()
+ print "Done"
+
+if __name__ == "__main__":
+ _test()
--- /dev/null
+"""Represent a Sequence Feature holding info about a part of a sequence.
+
+This is heavily modeled after the Biocorba SeqFeature objects, and
+may be pretty biased towards GenBank stuff since I'm writing it
+for the GenBank parser output...
+
+What's here:
+
+Base class to hold a Feature.
+----------------------------
+classes:
+o SeqFeature
+
+Hold information about a Reference.
+----------------------------------
+
+This is an attempt to create a General class to hold Reference type
+information.
+
+classes:
+o Reference
+
+Specify locations of a feature on a Sequence.
+---------------------------------------------
+
+This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in
+much the same way as Biocorba. This has the advantages of allowing us
+to handle fuzzy stuff in case anyone needs it, and also be compatible
+with Biocorba.
+
+classes:
+o FeatureLocation - Specify the start and end location of a feature.
+
+o ExactPosition - Specify the position as being exact.
+o WithinPosition - Specify a position occuring within some range.
+o BetweenPosition - Specify a position occuring between a range.
+o BeforePosition - Specify the position as being found before some base.
+o AfterPosition - Specify the position as being found after some base.
+"""
+
+class SeqFeature:
+ """Represent a Sequence Feature on an object.
+
+ Attributes:
+ o location - the location of the feature on the sequence
+ o type - the specified type of the feature (ie. CDS, exon, repeat...)
+ o location_operator - a string specifying how this SeqFeature may
+ be related to others. For example, in the example GenBank feature
+ shown below, the location_operator would be "join"
+ o strand - A value specifying on which strand (of a DNA sequence, for
+ instance) the feature deals with. 1 indicates the plus strand, -1
+ indicates the minus strand, 0 indicates both strands, and None indicates
+ that strand doesn't apply (ie. for proteins) or is not known.
+ o id - A string identifier for the feature.
+ o ref - A reference to another sequence. This could be an accession
+ number for some different sequence.
+ o ref_db - A different database for the reference accession number.
+ o qualifier - A dictionary of qualifiers on the feature. These are
+ analagous to the qualifiers from a GenBank feature table. The keys of
+ the dictionary are qualifier names, the values are the qualifier
+ values.
+ o sub_features - Additional SeqFeatures which fall under this 'parent'
+ feature. For instance, if we having something like:
+
+ CDS join(1..10,30..40,50..60)
+
+ The the top level feature would be a CDS from 1 to 60, and the sub
+ features would be of 'CDS_join' type and would be from 1 to 10, 30 to
+ 40 and 50 to 60, respectively.
+ """
+ def __init__(self, location = None, type = '', location_operator = '',
+ strand = None, id = "<unknown id>",
+ qualifiers = {}, sub_features = [],
+ ref = None, ref_db = None):
+ """Initialize a SeqFeature on a Sequence.
+ """
+ self.location = location
+
+ self.type = type
+ self.location_operator = location_operator
+ self.strand = strand
+ self.id = id
+ # XXX right now sub_features and qualifiers cannot be set
+ # from the initializer because this causes all kinds
+ # of recursive import problems. I can't understand why this is
+ # at all :-<
+ self.qualifiers = {}
+ self.sub_features = []
+ self.ref = ref
+ self.ref_db = ref_db
+
+ def __repr__(self):
+ """A string representation of the record for debugging."""
+ answer = "%s(%s" % (self.__class__, repr(self.location))
+ if self.type :
+ answer += ", type=%s" % repr(self.type)
+ if self.location_operator :
+ answer += ", location_operator=%s" % repr(self.location_operator)
+ if self.strand :
+ answer += ", strand=%s" % repr(self.strand)
+ if self.id and self.id != "<unknown id>" :
+ answer += ", id=%s" % repr(self.id)
+ if self.ref :
+ answer += ", ref=%s" % repr(self.ref)
+ if self.ref_db :
+ answer += ", ref_db=%s" % repr(self.ref_db)
+ answer += ")"
+ return answer
+
+ def __str__(self):
+ """A readable summary of the feature intended to be printed to screen.
+ """
+ out = "type: %s\n" % self.type
+ out += "location: %s\n" % self.location
+ out += "ref: %s:%s\n" % (self.ref, self.ref_db)
+ out += "strand: %s\n" % self.strand
+ out += "qualifiers: \n"
+ qualifier_keys = self.qualifiers.keys()
+ qualifier_keys.sort()
+ for qual_key in qualifier_keys:
+ out += "\tKey: %s, Value: %s\n" % (qual_key,
+ self.qualifiers[qual_key])
+ if len(self.sub_features) != 0:
+ out += "Sub-Features\n"
+ for sub_feature in self.sub_features:
+ out +="%s\n" % sub_feature
+
+ return out
+
+ def _shift(self, offset) :
+ """Returns a copy of the feature with its location shifted (PRIVATE).
+
+ The annotation qaulifiers are copied."""
+ answer = SeqFeature(location = self.location._shift(offset),
+ type = self.type,
+ location_operator = self.location_operator,
+ strand = self.strand,
+ id = self.id,
+ #qualifiers = dict(self.qualifiers.iteritems()),
+ #sub_features = [f._shift(offset) for f in self.sub_features],
+ ref = self.ref,
+ ref_db = self.ref_db)
+ #TODO - Sort out the use of sub_feature and qualifiers in __init___
+ answer.sub_features = [f._shift(offset) for f in self.sub_features]
+ answer.qualifiers = dict(self.qualifiers.iteritems())
+ return answer
+
+# --- References
+
+# TODO -- Will this hold PubMed and Medline information decently?
+class Reference:
+ """Represent a Generic Reference object.
+
+ Attributes:
+ o location - A list of Location objects specifying regions of
+ the sequence that the references correspond to. If no locations are
+ specified, the entire sequence is assumed.
+ o authors - A big old string, or a list split by author, of authors
+ for the reference.
+ o title - The title of the reference.
+ o journal - Journal the reference was published in.
+ o medline_id - A medline reference for the article.
+ o pubmed_id - A pubmed reference for the article.
+ o comment - A place to stick any comments about the reference.
+ """
+ def __init__(self):
+ self.location = []
+ self.authors = ''
+ self.consrtm = ''
+ self.title = ''
+ self.journal = ''
+ self.medline_id = ''
+ self.pubmed_id = ''
+ self.comment = ''
+
+ def __str__(self):
+ """Output an informative string for debugging.
+ """
+ out = ""
+ for single_location in self.location:
+ out += "location: %s\n" % single_location
+ out += "authors: %s\n" % self.authors
+ if self.consrtm:
+ out += "consrtm: %s\n" % self.consrtm
+ out += "title: %s\n" % self.title
+ out += "journal: %s\n" % self.journal
+ out += "medline id: %s\n" % self.medline_id
+ out += "pubmed id: %s\n" % self.pubmed_id
+ out += "comment: %s\n" % self.comment
+
+ return out
+
+# --- Handling feature locations
+
+class FeatureLocation:
+ """Specify the location of a feature along a sequence.
+
+ This attempts to deal with fuzziness of position ends, but also
+ make it easy to get the start and end in the 'normal' case (no
+ fuzziness).
+
+ You should access the start and end attributes with
+ your_location.start and your_location.end. If the start and
+ end are exact, this will return the positions, if not, we'll return
+ the approriate Fuzzy class with info about the position and fuzziness.
+
+ Note that the start and end location numbering follow Python's scheme,
+ thus a GenBank entry of 123..150 (one based counting) becomes a location
+ of [122:150] (zero based counting).
+ """
+ def __init__(self, start, end):
+ """Specify the start and end of a sequence feature.
+
+ start and end arguments specify the values where the feature begins
+ and ends. These can either by any of the *Position objects that
+ inherit from AbstractPosition, or can just be integers specifying the
+ position. In the case of integers, the values are assumed to be
+ exact and are converted in ExactPosition arguments. This is meant
+ to make it easy to deal with non-fuzzy ends.
+ """
+ if isinstance(start, AbstractPosition):
+ self._start = start
+ else:
+ self._start = ExactPosition(start)
+
+ if isinstance(end, AbstractPosition):
+ self._end = end
+ else:
+ self._end = ExactPosition(end)
+
+ def __str__(self):
+ """Returns a representation of the location (with python counting).
+
+ For the simple case this uses the python splicing syntax, [122:150]
+ (zero based counting) which GenBank would call 123..150 (one based
+ counting).
+ """
+ return "[%s:%s]" % (self._start, self._end)
+
+ def __repr__(self):
+ """A string representation of the location for debugging."""
+ return "%s(%s,%s)" \
+ % (self.__class__, repr(self.start), repr(self.end))
+
+ def _shift(self, offset) :
+ """Returns a copy of the location shifted by the offset (PRIVATE)."""
+ return FeatureLocation(start = self._start._shift(offset),
+ end = self._end._shift(offset))
+
+ def __getattr__(self, attr):
+ """Make it easy to get non-fuzzy starts and ends.
+
+ We override get_attribute here so that in non-fuzzy cases we
+ can just return the start and end position without any hassle.
+
+ To get fuzzy start and ends, just ask for item.start and
+ item.end. To get non-fuzzy attributes (ie. the position only)
+ ask for 'item.nofuzzy_start', 'item.nofuzzy_end'. These should return
+ the largest range of the fuzzy position. So something like:
+ (10.20)..(30.40) should return 10 for start, and 40 for end.
+
+ The special tricky case where is when we have a single between position
+ argument like 2^3 for the range. We want nofuzzy_start and nofuzzy_end
+ to give a reasonable approximation of what this really means, which
+ is an empty string -- so the same position for both. Doing a special
+ case here sucks, but there is really not a general rule you can apply
+ to this.
+ """
+ #TODO - these are not currently implemented as properties, this means
+ #they do not show up via dir(...)
+ if attr == 'start':
+ return self._start
+ elif attr == 'end':
+ return self._end
+ elif attr == 'nofuzzy_start':
+ if ((self._start == self._end) and isinstance(self._start,
+ BetweenPosition)):
+ return self._start.position
+ else:
+ return min(self._start.position,
+ self._start.position + self._start.extension)
+ elif attr == 'nofuzzy_end':
+ if ((self._start == self._end) and isinstance(self._start,
+ BetweenPosition)):
+ return self._end.position
+ else:
+ return max(self._end.position,
+ self._end.position + self._end.extension)
+ else:
+ raise AttributeError("Cannot evaluate attribute %s." % attr)
+
+class AbstractPosition:
+ """Abstract base class representing a position.
+ """
+ def __init__(self, position, extension):
+ self.position = position
+ self.extension = extension
+
+ def __repr__(self) :
+ """String representation of the location for debugging."""
+ return "%s(%s,%s)" \
+ % (self.__class__, repr(self.position), repr(self.extension))
+
+ def __cmp__(self, other):
+ """A simple comparison function for positions.
+
+ This is very simple-minded and just compares the position attribute
+ of the features; extensions are not considered at all. This could
+ potentially be expanded to try to take advantage of extensions.
+ """
+ assert isinstance(other, AbstractPosition), \
+ "We can only do comparisons between Biopython Position objects."
+
+ return cmp(self.position, other.position)
+
+ def _shift(self, offset) :
+ #We want this to maintain the subclass when called from a subclass
+ return self.__class__(self.position + offset, self.extension)
+
+class ExactPosition(AbstractPosition):
+ """Specify the specific position of a boundary.
+
+ o position - The position of the boundary.
+ o extension - An optional argument which must be zero since we don't
+ have an extension. The argument is provided so that the same number of
+ arguments can be passed to all position types.
+
+ In this case, there is no fuzziness associated with the position.
+ """
+ def __init__(self, position, extension = 0):
+ if extension != 0:
+ raise AttributeError("Non-zero extension %s for exact position."
+ % extension)
+ AbstractPosition.__init__(self, position, 0)
+
+ def __repr__(self) :
+ """String representation of the ExactPosition location for debugging."""
+ assert self.extension == 0
+ return "%s(%s)" % (self.__class__, repr(self.position))
+
+ def __str__(self):
+ return str(self.position)
+
+class WithinPosition(AbstractPosition):
+ """Specify the position of a boundary within some coordinates.
+
+ Arguments:
+ o position - The start position of the boundary
+ o extension - The range to which the boundary can extend.
+
+ This allows dealing with a position like ((1.4)..100). This
+ indicates that the start of the sequence is somewhere between 1
+ and 4. To represent that with this class we would set position as
+ 1 and extension as 3.
+ """
+ def __init__(self, position, extension = 0):
+ AbstractPosition.__init__(self, position, extension)
+
+ def __str__(self):
+ return "(%s.%s)" % (self.position, self.position + self.extension)
+
+class BetweenPosition(AbstractPosition):
+ """Specify the position of a boundary between two coordinates.
+
+ Arguments:
+ o position - The start position of the boundary.
+ o extension - The range to the other position of a boundary.
+
+ This specifies a coordinate which is found between the two positions.
+ So this allows us to deal with a position like ((1^2)..100). To
+ represent that with this class we set position as 1 and the
+ extension as 1.
+ """
+ def __init__(self, position, extension = 0):
+ AbstractPosition.__init__(self, position, extension)
+
+ def __str__(self):
+ return "(%s^%s)" % (self.position, self.position + self.extension)
+
+class BeforePosition(AbstractPosition):
+ """Specify a position where the actual location occurs before it.
+
+ Arguments:
+ o position - The upper boundary of where the location can occur.
+ o extension - An optional argument which must be zero since we don't
+ have an extension. The argument is provided so that the same number of
+ arguments can be passed to all position types.
+
+ This is used to specify positions like (<10..100) where the location
+ occurs somewhere before position 10.
+ """
+ def __init__(self, position, extension = 0):
+ if extension != 0:
+ raise AttributeError("Non-zero extension %s for exact position."
+ % extension)
+ AbstractPosition.__init__(self, position, 0)
+
+ def __repr__(self) :
+ """A string representation of the location for debugging."""
+ assert self.extension == 0
+ return "%s(%s)" % (self.__class__, repr(self.position))
+
+ def __str__(self):
+ return "<%s" % self.position
+
+class AfterPosition(AbstractPosition):
+ """Specify a position where the actual location is found after it.
+
+ Arguments:
+ o position - The lower boundary of where the location can occur.
+ o extension - An optional argument which must be zero since we don't
+ have an extension. The argument is provided so that the same number of
+ arguments can be passed to all position types.
+
+ This is used to specify positions like (>10..100) where the location
+ occurs somewhere after position 10.
+ """
+ def __init__(self, position, extension = 0):
+ if extension != 0:
+ raise AttributeError("Non-zero extension %s for exact position."
+ % extension)
+ AbstractPosition.__init__(self, position, 0)
+
+ def __repr__(self) :
+ """A string representation of the location for debugging."""
+ assert self.extension == 0
+ return "%s(%s)" % (self.__class__, repr(self.position))
+
+ def __str__(self):
+ return ">%s" % self.position
+
+class OneOfPosition(AbstractPosition):
+ """Specify a position where the location can be multiple positions.
+
+ This models the GenBank 'one-of(1888,1901)' function, and tries
+ to make this fit within the Biopython Position models. In our case
+ the position of the "one-of" is set as the lowest choice, and the
+ extension is the range to the highest choice.
+ """
+ def __init__(self, position_list):
+ """Initialize with a set of posssible positions.
+
+ position_list is a list of AbstractPosition derived objects,
+ specifying possible locations.
+ """
+ # unique attribute for this type of positions
+ self.position_choices = position_list
+ # find the smallest and largest position in the choices
+ smallest = None
+ largest = None
+ for position_choice in self.position_choices:
+ assert isinstance(position_choice, AbstractPosition), \
+ "Expected position objects, got %r" % position_choice
+ if smallest is None and largest is None:
+ smallest = position_choice.position
+ largest = position_choice.position
+ elif position_choice.position > largest:
+ largest = position_choice.position
+ elif position_choice.position < smallest:
+ smallest = position_choice.position
+ # initialize with our definition of position and extension
+ AbstractPosition.__init__(self, smallest, largest - smallest)
+
+ def __repr__(self) :
+ """String representation of the OneOfPosition location for debugging."""
+ return "%s(%s)" % (self.__class__, repr(self.position_choices))
+
+ def __str__(self):
+ out = "one-of("
+ for position in self.position_choices:
+ out += "%s," % position
+ # replace the last comma with the closing parenthesis
+ out = out[:-1] + ")"
+ return out
+
+class PositionGap:
+ """Simple class to hold information about a gap between positions.
+ """
+ def __init__(self, gap_size):
+ """Intialize with a position object containing the gap information.
+ """
+ self.gap_size = gap_size
+
+ def __repr__(self) :
+ """A string representation of the position gap for debugging."""
+ return "%s(%s)" % (self.__class__, repr(self.gap_size))
+
+ def __str__(self):
+ out = "gap(%s)" % self.gap_size
+ return out
--- /dev/null
+# Copyright 2008 by Peter Cock. All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Bio.SeqIO support for the "ace" file format.
+
+You are expected to use this module via the Bio.SeqIO functions.
+See also the Bio.Sequencing.Ace module which offers more than just accessing
+the contig consensus sequences in an ACE file as SeqRecord objects."""
+
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.Alphabet import generic_nucleotide, generic_dna, generic_rna, Gapped
+from Bio.Sequencing import Ace
+
+#This is a generator function!
+def AceIterator(handle) :
+ """Returns SeqRecord objects from an ACE file.
+
+ This uses the Bio.Sequencing.Ace module to do the hard work. Note that
+ by iterating over the file in a single pass, we are forced to ignore any
+ WA, CT, RT or WR footer tags."""
+
+ for ace_contig in Ace.parse(handle) :
+ #Convert the ACE contig record into a SeqRecord...
+ consensus_seq_str = ace_contig.sequence
+ #Assume its DNA unless there is a U in it,
+ if "U" in consensus_seq_str :
+ if "T" in consensus_seq_str :
+ #Very odd! Error?
+ alpha = generic_ncleotide
+ else :
+ alpha = generic_rna
+ else :
+ alpha = generic_dna
+
+ if "*" in consensus_seq_str :
+ #For consistency with most other file formats, map
+ #any * gaps into 0 gaps.
+ assert "-" not in consensus_seq_str
+ consensus_seq = Seq(consensus_seq_str.replace("*","-"),
+ Gapped(alpha, gap_char="-"))
+ else :
+ consensus_seq = Seq(consensus_seq_str, alpha)
+
+ #TODO - Consensus base quality (BQ lines). Note that any gaps
+ #(* character) in the consensus does not get a quality entry.
+ #This really needs Biopython support for per-letter-annotation.
+
+ #TODO? - Base segments (BS lines) which indicates which read
+ #phrap has chosen to be the consensus at a particular position.
+ #Perhaps as SeqFeature objects?
+
+ #TODO - Supporting reads (RD lines, plus perhaps QA and DS lines)
+ #Perhaps as SeqFeature objects?
+
+ seq_record = SeqRecord(consensus_seq,
+ id = ace_contig.name,
+ name = ace_contig.name)
+ yield seq_record
+ #All done
--- /dev/null
+# Copyright 2006-2009 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+#
+# This module is for reading and writing FASTA format files as SeqRecord
+# objects. The code is partly inspired by earlier Biopython modules,
+# Bio.Fasta.* and the now deprecated Bio.SeqIO.FASTA
+
+"""Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.
+
+You are expected to use this module via the Bio.SeqIO functions."""
+
+from Bio.Alphabet import single_letter_alphabet
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Interfaces import SequentialSequenceWriter
+
+#This is a generator function!
+def FastaIterator(handle, alphabet = single_letter_alphabet, title2ids = None) :
+ """Generator function to iterate over Fasta records (as SeqRecord objects).
+
+ handle - input file
+ alphabet - optional alphabet
+ title2ids - A function that, when given the title of the FASTA
+ file (without the beginning >), will return the id, name and
+ description (in that order) for the record as a tuple of strings.
+
+ If this is not given, then the entire title line will be used
+ as the description, and the first word as the id and name.
+
+ Note that use of title2ids matches that of Bio.Fasta.SequenceParser
+ but the defaults are slightly different.
+ """
+ #Skip any text before the first record (e.g. blank lines, comments)
+ while True :
+ line = handle.readline()
+ if line == "" : return #Premature end of file, or just empty?
+ if line[0] == ">" :
+ break
+
+ while True :
+ if line[0]!=">" :
+ raise ValueError("Records in Fasta files should start with '>' character")
+ if title2ids :
+ id, name, descr = title2ids(line[1:].rstrip())
+ else :
+ descr = line[1:].rstrip()
+ id = descr.split()[0]
+ name = id
+
+ lines = []
+ line = handle.readline()
+ while True:
+ if not line : break
+ if line[0] == ">": break
+ #Remove trailing whitespace, and any internal spaces
+ #(and any embedded \r which are possible in mangled files
+ #when not opened in universal read lines mode)
+ lines.append(line.rstrip().replace(" ","").replace("\r",""))
+ line = handle.readline()
+
+ #Return the record and then continue...
+ yield SeqRecord(Seq("".join(lines), alphabet),
+ id = id, name = name, description = descr)
+
+ if not line : return #StopIteration
+ assert False, "Should not reach this line"
+
+class FastaWriter(SequentialSequenceWriter):
+ """Class to write Fasta format files."""
+ def __init__(self, handle, wrap=60, record2title=None):
+ """Create a Fasta writer.
+
+ handle - Handle to an output file, e.g. as returned
+ by open(filename, "w")
+ wrap - Optional line length used to wrap sequence lines.
+ Defaults to wrapping the sequence at 60 characters
+ Use zero (or None) for no wrapping, giving a single
+ long line for the sequence.
+ record2title - Optional function to return the text to be
+ used for the title line of each record. By default the
+ a combination of the record.id and record.description
+ is used. If the record.description starts with the
+ record.id, then just the record.description is used.
+
+ You can either use:
+
+ myWriter = FastaWriter(open(filename,"w"))
+ writer.write_file(myRecords)
+
+ Or, follow the sequential file writer system, for example:
+
+ myWriter = FastaWriter(open(filename,"w"))
+ writer.write_header() # does nothing for Fasta files
+ ...
+ Multiple calls to writer.write_record() and/or writer.write_records()
+ ...
+ writer.write_footer() # does nothing for Fasta files
+ writer.close()
+ """
+ SequentialSequenceWriter.__init__(self, handle)
+ #self.handle = handle
+ self.wrap = None
+ if wrap :
+ if wrap < 1 :
+ raise ValueError
+ self.wrap = wrap
+ self.record2title = record2title
+
+ def write_record(self, record):
+ """Write a single Fasta record to the file."""
+ assert self._header_written
+ assert not self._footer_written
+ self._record_written = True
+
+ if self.record2title :
+ title=self.clean(self.record2title(record))
+ else :
+ id = self.clean(record.id)
+ description = self.clean(record.description)
+
+ #if description[:len(id)]==id :
+ if description and description.split(None,1)[0]==id :
+ #The description includes the id at the start
+ title = description
+ else :
+ title = "%s %s" % (id, description)
+
+ assert "\n" not in title
+ assert "\r" not in title
+ self.handle.write(">%s\n" % title)
+
+ data = self._get_seq_string(record) #Catches sequence being None
+
+ assert "\n" not in data
+ assert "\r" not in data
+
+ if self.wrap :
+ for i in range(0, len(data), self.wrap):
+ self.handle.write(data[i:i+self.wrap] + "\n")
+ else :
+ self.handle.write(data + "\n")
+
+if __name__ == "__main__" :
+ print "Running quick self test"
+
+ import os
+ from Bio.Alphabet import generic_protein, generic_nucleotide
+
+ #Download the files from here:
+ #ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans
+ fna_filename = "NC_005213.fna"
+ faa_filename = "NC_005213.faa"
+
+ def genbank_name_function(text) :
+ text, descr = text.split(None,1)
+ id = text.split("|")[3]
+ name = id.split(".",1)[0]
+ return id, name, descr
+
+ def print_record(record) :
+ #See also bug 2057
+ #http://bugzilla.open-bio.org/show_bug.cgi?id=2057
+ print "ID:" + record.id
+ print "Name:" + record.name
+ print "Descr:" + record.description
+ print record.seq
+ for feature in record.annotations :
+ print '/%s=%s' % (feature, record.annotations[feature])
+ if record.dbxrefs :
+ print "Database cross references:"
+ for x in record.dbxrefs : print " - %s" % x
+
+ if os.path.isfile(fna_filename) :
+ print "--------"
+ print "FastaIterator (single sequence)"
+ iterator = FastaIterator(open(fna_filename, "r"), alphabet=generic_nucleotide, title2ids=genbank_name_function)
+ count=0
+ for record in iterator :
+ count=count+1
+ print_record(record)
+ assert count == 1
+ print str(record.__class__)
+
+ if os.path.isfile(faa_filename) :
+ print "--------"
+ print "FastaIterator (multiple sequences)"
+ iterator = FastaIterator(open(faa_filename, "r"), alphabet=generic_protein, title2ids=genbank_name_function)
+ count=0
+ for record in iterator :
+ count=count+1
+ print_record(record)
+ break
+ assert count>0
+ print str(record.__class__)
+
+ from cStringIO import StringIO
+ print "--------"
+ print "FastaIterator (empty input file)"
+ #Just to make sure no errors happen
+ iterator = FastaIterator(StringIO(""))
+ count = 0
+ for record in iterator :
+ count = count+1
+ assert count==0
+
+ print "Done"
--- /dev/null
+# Copyright 2008 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+#
+# This module is for reading and writing IntelliGenetics format files as
+# SeqRecord objects. This file format appears to be the same as the MASE
+# multiple sequence alignment format.
+
+"""Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.
+
+You are expected to use this module via the Bio.SeqIO functions."""
+
+from Bio.Alphabet import single_letter_alphabet
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+#This is a generator function!
+def IgIterator(handle, alphabet = single_letter_alphabet) :
+ """Iterate over IntelliGenetics records (as SeqRecord objects).
+
+ handle - input file
+ alphabet - optional alphabet
+
+ The optional free format file header lines (which start with two
+ semi-colons) are ignored.
+
+ The free format commentary lines at the start of each record (which
+ start with a semi-colon) are recorded as a single string with embedded
+ new line characters in the SeqRecord's annotations dictionary under the
+ key 'comment'.
+ """
+ #Skip any file header text before the first record (;; lines)
+ while True :
+ line = handle.readline()
+ if not line : break #Premature end of file, or just empty?
+ if not line.startswith(";;") : break
+
+ while line :
+ #Now iterate over the records
+ if line[0]!=";" :
+ raise ValueError( \
+ "Records should start with ';' and not:\n%s" % repr(line))
+
+ #Try and agree with SeqRecord convention from the GenBank parser,
+ #(and followed in the SwissProt parser) which stores the comments
+ #as a long string with newlines under annotations key 'comment'.
+
+ #Note some examples use "; ..." and others ";..."
+ comment_lines = []
+ while line.startswith(";") :
+ #TODO - Extract identifier from lines like "LOCUS\tB_SF2"?
+ comment_lines.append(line[1:].strip())
+ line = handle.readline()
+ title = line.rstrip()
+
+ seq_lines = []
+ while True:
+ line = handle.readline()
+ if not line : break
+ if line[0] == ";": break
+ #Remove trailing whitespace, and any internal spaces
+ seq_lines.append(line.rstrip().replace(" ",""))
+ seq_str = "".join(seq_lines)
+ if seq_str.endswith("1") :
+ #Remove the optional terminator (digit one)
+ seq_str = seq_str[:-1]
+ if "1" in seq_str :
+ raise ValueError("Potential terminator digit one found within sequence.")
+
+ #Return the record and then continue...
+ record= SeqRecord(Seq(seq_str, alphabet),
+ id = title, name = title)
+ record.annotations['comment'] = "\n".join(comment_lines)
+ yield record
+
+ #We should be at the end of the file now
+ assert not line
+
+if __name__ == "__main__" :
+ print "Running quick self test"
+
+ import os
+ path = "../../Tests/IntelliGenetics/"
+ if os.path.isdir(path) :
+ for filename in os.listdir(path) :
+ if os.path.splitext(filename)[-1] == ".txt" :
+ print
+ print filename
+ print "-"*len(filename)
+ handle = open(os.path.join(path, filename))
+ for record in IgIterator(handle) :
+ print record.id, len(record)
+ handle.close()
+ print "Done"
+ else :
+ print "Could not find input files"
--- /dev/null
+# Copyright 2007-2009 by Peter Cock. All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package..
+
+"""Bio.SeqIO support for the "genbank" and "embl" file formats.
+
+You are expected to use this module via the Bio.SeqIO functions.
+Note that internally this module calls Bio.GenBank to do the actual
+parsing of both GenBank and EMBL files.
+
+See also:
+
+International Nucleotide Sequence Database Collaboration
+http://www.insdc.org/
+
+GenBank
+http://www.ncbi.nlm.nih.gov/Genbank/
+
+EMBL Nucleotide Sequence Database
+http://www.ebi.ac.uk/embl/
+
+DDBJ (DNA Data Bank of Japan)
+http://www.ddbj.nig.ac.jp/
+"""
+
+from Bio.Seq import UnknownSeq
+from Bio.GenBank.Scanner import GenBankScanner, EmblScanner
+from Bio import Alphabet
+from Interfaces import SequentialSequenceWriter
+
+# NOTE
+# ====
+# The "brains" for parsing GenBank and EMBL files (and any
+# other flat file variants from the INSDC in future) is in
+# Bio.GenBank.Scanner (plus the _FeatureConsumer in Bio.GenBank)
+
+def GenBankIterator(handle) :
+ """Breaks up a Genbank file into SeqRecord objects.
+
+ Every section from the LOCUS line to the terminating // becomes
+ a single SeqRecord with associated annotation and features.
+
+ Note that for genomes or chromosomes, there is typically only
+ one record."""
+ #This calls a generator function:
+ return GenBankScanner(debug=0).parse_records(handle)
+
+def EmblIterator(handle) :
+ """Breaks up an EMBL file into SeqRecord objects.
+
+ Every section from the LOCUS line to the terminating // becomes
+ a single SeqRecord with associated annotation and features.
+
+ Note that for genomes or chromosomes, there is typically only
+ one record."""
+ #This calls a generator function:
+ return EmblScanner(debug=0).parse_records(handle)
+
+def GenBankCdsFeatureIterator(handle, alphabet=Alphabet.generic_protein) :
+ """Breaks up a Genbank file into SeqRecord objects for each CDS feature.
+
+ Every section from the LOCUS line to the terminating // can contain
+ many CDS features. These are returned as with the stated amino acid
+ translation sequence (if given).
+ """
+ #This calls a generator function:
+ return GenBankScanner(debug=0).parse_cds_features(handle, alphabet)
+
+def EmblCdsFeatureIterator(handle, alphabet=Alphabet.generic_protein) :
+ """Breaks up a EMBL file into SeqRecord objects for each CDS feature.
+
+ Every section from the LOCUS line to the terminating // can contain
+ many CDS features. These are returned as with the stated amino acid
+ translation sequence (if given).
+ """
+ #This calls a generator function:
+ return EmblScanner(debug=0).parse_cds_features(handle, alphabet)
+
+class GenBankWriter(SequentialSequenceWriter) :
+ HEADER_WIDTH = 12
+ MAX_WIDTH = 80
+
+ def _write_single_line(self, tag, text) :
+ "Used in the the 'header' of each GenBank record."""
+ assert len(tag) < self.HEADER_WIDTH
+ assert len(text) < self.MAX_WIDTH - self.HEADER_WIDTH, \
+ "Annotation %s too long for %s line" % (repr(text), tag)
+ self.handle.write("%s%s\n" % (tag.ljust(self.HEADER_WIDTH),
+ text.replace("\n"," ")))
+
+ def _write_multi_line(self, tag, text) :
+ "Used in the the 'header' of each GenBank record."""
+ #TODO - Do the line spliting while preserving white space?
+ max_len = self.MAX_WIDTH - self.HEADER_WIDTH
+ assert len(tag) < self.HEADER_WIDTH
+ text = text.strip()
+ if len(text) < max_len :
+ self._write_single_line(tag, text)
+ return
+
+ words = text.split()
+ assert max([len(w) for w in words]) < max_len, \
+ "Your description cannot be broken into nice lines!"
+ text = ""
+ while words and len(text) + 1 + len(words[0]) < max_len :
+ text += " " + words.pop(0)
+ text = text.strip()
+ assert len(text) < max_len
+ self._write_single_line(tag, text)
+ while words :
+ text = ""
+ while words and len(text) + 1 + len(words[0]) < max_len :
+ text += " " + words.pop(0)
+ text = text.strip()
+ assert len(text) < max_len
+ self._write_single_line("", text)
+ assert not words
+
+ def _write_the_first_line(self, record) :
+ """Write the LOCUS line."""
+
+ locus = record.name
+ if not locus or locus == "<unknown name>" :
+ locus = record.id
+ if not locus or locus == "<unknown id>" :
+ locus = self._get_annotation_str(record, "accession", just_first=True)
+ if len(locus) > 16 :
+ raise ValueError("Locus identifier %s is too long" % repr(locus))
+
+ if len(record) > 99999999999 :
+ #Currently GenBank only officially support up to 350000, but
+ #the length field can take eleven digits
+ raise ValueError("Sequence too long!")
+
+ #Get the base alphabet (underneath any Gapped or StopCodon encoding)
+ a = Alphabet._get_base_alphabet(record.seq.alphabet)
+ if not isinstance(a, Alphabet.Alphabet) :
+ raise TypeError("Invalid alphabet")
+ elif isinstance(a, Alphabet.ProteinAlphabet) :
+ units = "bp"
+ elif isinstance(a, Alphabet.NucleotideAlphabet) :
+ units = "aa"
+ else :
+ #Must be something like NucleotideAlphabet or
+ #just the generic Alphabet (default for fasta files)
+ raise ValueError("Need a Nucleotide or Protein alphabet")
+
+ #Get the molecule type
+ #TODO - record this explicitly in the parser?
+ if isinstance(a, Alphabet.ProteinAlphabet) :
+ mol_type = ""
+ elif isinstance(a, Alphabet.DNAAlphabet) :
+ mol_type = "DNA"
+ elif isinstance(a, Alphabet.RNAAlphabet) :
+ mol_type = "RNA"
+ else :
+ #Must be something like NucleotideAlphabet or
+ #just the generic Alphabet (default for fasta files)
+ raise ValueError("Need a DNA, RNA or Protein alphabet")
+
+ try :
+ division = record.annotations["data_file_division"]
+ except KeyError :
+ division = "UNK"
+ if division not in ["PRI","ROD","MAM","VRT","INV","PLN","BCT",
+ "VRL","PHG","SYN","UNA","EST","PAT","STS",
+ "GSS","HTG","HTC","ENV"] :
+ division = "UNK"
+
+ assert len(units) == 2
+ assert len(division) == 3
+ #TODO - date
+ #TODO - mol_type
+ line = "LOCUS %s %s %s %s %s 01-JAN-1980\n" \
+ % (locus.ljust(16),
+ str(len(record)).rjust(11),
+ units,
+ mol_type.ljust(6),
+ division)
+ assert len(line) == 79+1, repr(line) #plus one for new line
+
+ assert line[12:28].rstrip() == locus, \
+ 'LOCUS line does not contain the locus at the expected position:\n' + line
+ assert line[28:29] == " "
+ assert line[29:40].lstrip() == str(len(record)), \
+ 'LOCUS line does not contain the length at the expected position:\n' + line
+
+ #Tests copied from Bio.GenBank.Scanner
+ assert line[40:44] in [' bp ', ' aa '] , \
+ 'LOCUS line does not contain size units at expected position:\n' + line
+ assert line[44:47] in [' ', 'ss-', 'ds-', 'ms-'], \
+ 'LOCUS line does not have valid strand type (Single stranded, ...):\n' + line
+ assert line[47:54].strip() == "" \
+ or line[47:54].strip().find('DNA') != -1 \
+ or line[47:54].strip().find('RNA') != -1, \
+ 'LOCUS line does not contain valid sequence type (DNA, RNA, ...):\n' + line
+ assert line[54:55] == ' ', \
+ 'LOCUS line does not contain space at position 55:\n' + line
+ assert line[55:63].strip() in ['','linear','circular'], \
+ 'LOCUS line does not contain valid entry (linear, circular, ...):\n' + line
+ assert line[63:64] == ' ', \
+ 'LOCUS line does not contain space at position 64:\n' + line
+ assert line[67:68] == ' ', \
+ 'LOCUS line does not contain space at position 68:\n' + line
+ assert line[70:71] == '-', \
+ 'LOCUS line does not contain - at position 71 in date:\n' + line
+ assert line[74:75] == '-', \
+ 'LOCUS line does not contain - at position 75 in date:\n' + line
+
+ self.handle.write(line)
+
+ def _get_annotation_str(self, record, key, default=".", just_first=False) :
+ """Get an annotation dictionary entry (as a string).
+
+ Some entries are lists, in which case if just_first=True the first entry
+ is returned. If just_first=False (default) this verifies there is only
+ one entry before returning it."""
+ try :
+ answer = record.annotations[key]
+ except KeyError :
+ return default
+ if isinstance(answer, list) :
+ if not just_first : assert len(answer) == 1
+ return str(answer[0])
+ else :
+ return str(answer)
+
+ def _write_sequence(self, record):
+ #Loosely based on code from Howard Salis
+ #TODO - Force lower case?
+ LETTERS_PER_LINE = 60
+ SEQUENCE_INDENT = 9
+
+ if isinstance(record.seq, UnknownSeq) :
+ #We have already recorded the length, and there is no need
+ #to record a long sequence of NNNNNNN...NNN or whatever.
+ return
+
+ data = self._get_seq_string(record) #Catches sequence being None
+ seq_len = len(data)
+ for line_number in range(0,seq_len,LETTERS_PER_LINE):
+ self.handle.write(str(line_number+1).rjust(SEQUENCE_INDENT))
+ for words in range(line_number,min(line_number+LETTERS_PER_LINE,seq_len),10):
+ self.handle.write(" %s" % data[words:words+10])
+ self.handle.write("\n")
+
+ def write_record(self, record):
+ """Write a single record to the output file."""
+ handle = self.handle
+ self._write_the_first_line(record)
+
+ accession = self._get_annotation_str(record, "accession",
+ record.id.split(".",1)[0],
+ just_first=True)
+ acc_with_version = accession
+ if record.id.startswith(accession+".") :
+ try :
+ acc_with_version = "%s.%i" \
+ % (accession, int(record.id.split(".",1)[1]))
+ except ValueError :
+ pass
+ gi = self._get_annotation_str(record, "gi", just_first=True)
+
+ descr = record.description
+ if descr == "<unknown description>" : descr = "."
+ self._write_multi_line("DEFINITION", descr)
+
+ self._write_single_line("ACCESSION", accession)
+ if gi != "." :
+ self._write_single_line("VERSION", "%s GI:%s" % (acc_with_version,gi))
+ else :
+ self._write_single_line("VERSION", "%s" % (acc_with_version))
+
+ try :
+ #List of strings
+ keywords = "; ".join(record.annotations["keywords"])
+ except KeyError :
+ keywords = "."
+ self._write_multi_line("KEYWORDS", keywords)
+
+ self._write_multi_line("SOURCE", \
+ self._get_annotation_str(record, "source"))
+ #The ORGANISM line MUST be a single line, as any continuation is the taxonomy
+ org = self._get_annotation_str(record, "organism")
+ if len(org) > self.MAX_WIDTH - self.HEADER_WIDTH :
+ org = org[:self.MAX_WIDTH - self.HEADER_WIDTH-4]+"..."
+ self._write_single_line(" ORGANISM", org)
+ try :
+ #List of strings
+ taxonomy = "; ".join(record.annotations["taxonomy"])
+ except KeyError :
+ taxonomy = "."
+ self._write_multi_line("", taxonomy)
+
+ #TODO - References...
+ handle.write("FEATURES Location/Qualifiers\n")
+ for feature in record.features :
+ self._write_feature(feature)
+ handle.write("ORIGIN\n")
+ self._write_sequence(record)
+ handle.write("//\n")
+
+ def _write_feature(self, feature):
+ """Write a single SeqFeature object to features table.
+
+ Not implemented yet, but this stub exists in the short term to
+ facilitate working on writing GenBank files with a sub-class."""
+ #TODO - Features...
+ pass
+
+if __name__ == "__main__" :
+ print "Quick self test"
+ import os
+ from StringIO import StringIO
+
+ def check_genbank_writer(records) :
+ handle = StringIO()
+ GenBankWriter(handle).write_file(records)
+ handle.seek(0)
+
+ records2 = list(GenBankIterator(handle))
+
+ assert len(records) == len(records2)
+ for r1, r2 in zip(records, records2) :
+ #The SwissProt parser may leave \n in the description...
+ assert r1.description.replace("\n", " ") == r2.description
+ assert r1.id == r2.id
+ assert r1.name == r2.name
+ assert str(r1.seq) == str(r2.seq)
+ for key in ["gi", "keywords", "source", "taxonomy"] :
+ if key in r1.annotations :
+ assert r1.annotations[key] == r2.annotations[key], key
+ for key in ["organism"] :
+ if key in r1.annotations :
+ v1 = r1.annotations[key]
+ v2 = r2.annotations[key]
+ assert isinstance(v1, str) and isinstance(v2, str)
+ #SwissProt organism can be too long to record in GenBank format
+ assert v1 == v2 or \
+ (v2.endswith("...") and v1.startswith(v2[:-3])), key
+
+ for filename in os.listdir("../../Tests/GenBank") :
+ if not filename.endswith(".gbk") and not filename.endswith(".gb") :
+ continue
+ print filename
+
+ handle = open("../../Tests/GenBank/%s" % filename)
+ records = list(GenBankIterator(handle))
+ handle.close()
+
+ check_genbank_writer(records)
+
+ for filename in os.listdir("../../Tests/EMBL") :
+ if not filename.endswith(".embl") :
+ continue
+ print filename
+
+ handle = open("../../Tests/EMBL/%s" % filename)
+ records = list(EmblIterator(handle))
+ handle.close()
+
+ check_genbank_writer(records)
+
+ from Bio import SeqIO
+ for filename in os.listdir("../../Tests/SwissProt") :
+ if not filename.startswith("sp") :
+ continue
+ print filename
+
+ handle = open("../../Tests/SwissProt/%s" % filename)
+ records = list(SeqIO.parse(handle,"swiss"))
+ handle.close()
+
+ check_genbank_writer(records)
+
--- /dev/null
+# Copyright 2006-2008 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+"""
+Bio.SeqIO support module (not for general use).
+
+Unless you are writing a new parser or writer for Bio.SeqIO, you should not
+use this module. It provides base classes to try and simplify things.
+"""
+
+from Bio.Alphabet import generic_alphabet
+
+class SequenceIterator :
+ """Base class for building SeqRecord iterators.
+
+ You should write a next() method to return SeqRecord
+ objects. You may wish to redefine the __init__
+ method as well.
+ """
+ def __init__(self, handle, alphabet=generic_alphabet) :
+ """Create a SequenceIterator object.
+
+ handle - input file
+ alphabet - optional, e.g. Bio.Alphabet.generic_protein
+
+ Note when subclassing:
+ - there should be a single non-optional argument,
+ the handle.
+ - you do not have to require an alphabet.
+ - you can add additional optional arguments."""
+ self.handle = handle
+ self.alphabet = alphabet
+ #####################################################
+ # You may want to subclass this, for example #
+ # to read through the file to find the first record,#
+ # or if additional arguments are required. #
+ #####################################################
+
+ def next(self) :
+ """Return the next record in the file.
+
+ This method should be replaced by any derived class to do something useful."""
+ raise NotImplementedError("This object should be subclassed")
+ #####################################################
+ # You SHOULD subclass this, to split the file up #
+ # into your individual records, and convert these #
+ # into useful objects, e.g. return SeqRecord object #
+ #####################################################
+
+ def __iter__(self):
+ """Iterate over the entries as a SeqRecord objects.
+
+ Example usage for Fasta files:
+
+ myFile = open("example.fasta","r")
+ myFastaReader = FastaIterator(myFile)
+ for record in myFastaReader :
+ print record.id
+ print record.seq
+ myFile.close()"""
+ return iter(self.next, None)
+
+class InterlacedSequenceIterator(SequenceIterator) :
+ """Base class for any iterator of a non-sequential file type.
+
+ This object is not intended for use directly.
+
+ When writing a parser for any interlaced sequence file where the whole
+ file must be read in order to extract any single record, then you should
+ subclass this object.
+
+ All you need to do is to define your own:
+ (1) __init__ method to parse the file and call self.move_start()
+ (2) __len__ method to return the number of records
+ (3) __getitem__ to return any requested record.
+
+ This class will then provide the iterator methods including next(), but relies
+ on knowing the total number of records and tracking the pending record index in
+ as self._n
+
+ It is up to the subclassed object to decide if it wants to generate a cache of
+ SeqRecords when initialised, or simply use its own lists and dicts and create
+ SeqRecords on request.
+ """
+
+ def __init__(self) :
+ """Create the object.
+
+ This method should be replaced by any derived class to do something useful."""
+ #We assume that your implementation of __init__ will ensure self._n=0
+ self.move_start()
+ raise NotImplementedError("This object method should be subclassed")
+ #####################################################
+ # You SHOULD subclass this #
+ #####################################################
+
+ def __len__(self) :
+ """Return the number of records.
+
+ This method should be replaced by any derived class to do something useful."""
+ raise NotImplementedError("This object method should be subclassed")
+ #####################################################
+ # You SHOULD subclass this #
+ #####################################################
+
+ def __getitem__(self, i) :
+ """Return the requested record.
+
+ This method should be replaced by any derived class to do something
+ useful.
+
+ It should NOT touch the value of self._n"""
+ raise NotImplementedError("This object method should be subclassed")
+ #####################################################
+ # You SHOULD subclass this #
+ #####################################################
+
+ def move_start(self) :
+ self._n = 0
+
+ def next(self) :
+ next_record = self._n
+ if next_record < len(self) :
+ self._n = next_record+1
+ return self[next_record]
+ else :
+ #StopIteration
+ return None
+
+ def __iter__(self):
+ return iter(self.next, None)
+
+class SequenceWriter:
+ """This class should be subclassed.
+
+ Interlaced file formats (e.g. Clustal) should subclass directly.
+
+ Sequential file formats (e.g. Fasta, GenBank) should subclass
+ the SequentialSequenceWriter class instead.
+ """
+ def __init__(self, handle):
+ """Creates the writer object.
+
+ Use the method write_file() to actually record your sequence records."""
+ self.handle = handle
+
+ def _get_seq_string(self, record):
+ """Use this to catch errors like the sequence being None."""
+ try :
+ #The tostring() method is part of the Seq API, we could instead
+ #use str(record.seq) but that would give a string "None" if the
+ #sequence was None, and unpredicatable output if an unexpected
+ #object was present.
+ return record.seq.tostring()
+ except AttributeError :
+ if record.seq is None :
+ #We could silently treat this as an empty sequence, Seq(""),
+ #but that would be an implict assumption we should avoid.
+ raise TypeError("SeqRecord (id=%s) has None for its sequence." \
+ % record.id)
+ else :
+ raise TypeError("SeqRecord (id=%s) has an invalid sequence." \
+ % record.id)
+
+ def clean(self, text) :
+ """Use this to avoid getting newlines in the output."""
+ answer = text
+ for x in ["\n", "\r"] :
+ answer = answer.replace(x, " ")
+ return answer.replace(" ", " ")
+
+ def write_file(self, records) :
+ """Use this to write an entire file containing the given records.
+
+ records - A list or iterator returning SeqRecord objects
+
+ Should return the number of records (as an integer).
+
+ This method can only be called once."""
+ #Note when implementing this, you should close the file at the end.
+ raise NotImplementedError("This object should be subclassed")
+ #####################################################
+ # You SHOULD subclass this #
+ #####################################################
+
+class SequentialSequenceWriter(SequenceWriter):
+ """This class should be subclassed.
+
+ It is intended for sequential file formats with an (optional)
+ header, repeated records, and an (optional) footer.
+
+ In this case (as with interlaced file formats), the user may
+ simply call the write_file() method and be done.
+
+ However, they may also call the write_header(), followed
+ by multiple calls to write_record() and/or write_records()
+ followed finally by write_footer().
+
+ Users must call write_header() and write_footer() even when
+ the file format concerned doesn't have a header or footer.
+ This is to try and make life as easy as possible when
+ switching the output format.
+
+ Note that write_header() cannot require any assumptions about
+ the number of records.
+ """
+ def __init__(self, handle):
+ self.handle = handle
+ self._header_written = False
+ self._record_written = False
+ self._footer_written = False
+
+ def write_header(self) :
+ assert not self._header_written, "You have aleady called write_header()"
+ assert not self._record_written, "You have aleady called write_record() or write_records()"
+ assert not self._footer_written, "You have aleady called write_footer()"
+ self._header_written = True
+
+ def write_footer(self) :
+ assert self._header_written, "You must call write_header() first"
+ assert self._record_written, "You have not called write_record() or write_records() yet"
+ assert not self._footer_written, "You have aleady called write_footer()"
+ self._footer_written = True
+
+ def write_record(self, record):
+ """Write a single record to the output file.
+
+ record - a SeqRecord object
+
+ Once you have called write_header() you can call write_record()
+ and/or write_records() as many times as needed. Then call
+ write_footer() and close()."""
+ assert self._header_written, "You must call write_header() first"
+ assert not self._footer_written, "You have already called write_footer()"
+ self._record_written = True
+ raise NotImplementedError("This object should be subclassed")
+ #####################################################
+ # You SHOULD subclass this #
+ #####################################################
+
+ def write_records(self, records):
+ """Write multiple record to the output file.
+
+ records - A list or iterator returning SeqRecord objects
+
+ Once you have called write_header() you can call write_record()
+ and/or write_records() as many times as needed. Then call
+ write_footer() and close().
+
+ Returns the number of records written.
+ """
+ #Default implementation:
+ assert self._header_written, "You must call write_header() first"
+ assert not self._footer_written, "You have already called write_footer()"
+ count = 0
+ for record in records :
+ self.write_record(record)
+ count += 1
+ #Mark as true, even if there where no records
+ self._record_written = True
+ return count
+
+ def write_file(self, records) :
+ """Use this to write an entire file containing the given records.
+
+ records - A list or iterator returning SeqRecord objects
+
+ This method can only be called once. Returns the number of records
+ written.
+ """
+ self.write_header()
+ count = self.write_records(records)
+ self.write_footer()
+ return count
--- /dev/null
+# Copyright 2008 by Peter Cock. All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Bio.SeqIO support for the "phd" file format.
+
+PHD files are output by PHRED and used by PHRAP and CONSED.
+
+You are expected to use this module via the Bio.SeqIO functions.
+See also the underlying Bio.Sequencing.Phd module."""
+
+from Bio.SeqRecord import SeqRecord
+from Bio.Sequencing import Phd
+
+#This is a generator function!
+def PhdIterator(handle) :
+ """Returns SeqRecord objects from a PHD file.
+
+ This uses the Bio.Sequencing.Phy module to do the hard work.
+ """
+
+ phd_records = Phd.parse(handle)
+ for phd_record in phd_records:
+ #Convert the PHY record into a SeqRecord...
+ seq_record = SeqRecord(phd_record.seq,
+ id = phd_record.file_name,
+ name = phd_record.file_name)
+ #Just re-use the comments dictionary as the SeqRecord's annotations
+ seq_record.annotations = phd_record.comments
+ yield seq_record
+ #All done
+
+if __name__ == "__main__" :
+ print "Quick self test"
+ handle = open("../../Tests/Phd/Phd1")
+ for record in PhdIterator(handle) :
+ print record
+ handle.close()
+ print "Done"
+
+
--- /dev/null
+# Copyright 2008 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+#
+# This module is for reading and writing PIR or NBRF format files as
+# SeqRecord objects. The code is based on Bio.SeqIO.FastaIO
+
+"""Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format.
+
+You are expected to use this module via the Bio.SeqIO functions, or if
+the file contains a sequence alignment, optionally via Bio.AlignIO instead.
+
+This format was introduced for the Protein Information Resource (PIR), a
+project of the National Biomedical Research Foundation (NBRF). The PIR
+database itself is now part of UniProt.
+
+The file format is described online at:
+http://www.ebi.ac.uk/help/pir_frame.html
+http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html (currently down)
+
+An example file in this format would be:
+
+>P1;CRAB_ANAPL
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+ MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
+ SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
+ GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
+ SDVPERSIPI TREEKPAIAG AQRK*
+
+>P1;CRAB_BOVIN
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+ MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
+ PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
+ HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
+ QASGPERTIP ITREEKPAVT AAPKK*
+
+Or, an example of a multiple sequence alignment:
+
+>P1;S27231
+rhodopsin - northern leopard frog
+MNGTEGPNFY IPMSNKTGVV RSPFDYPQYY LAEPWKYSVL AAYMFLLILL GLPINFMTLY
+VTIQHKKLRT PLNYILLNLG VCNHFMVLCG FTITMYTSLH GYFVFGQTGC YFEGFFATLG
+GEIALWSLVV LAIERYIVVC KPMSNFRFGE NHAMMGVAFT WIMALACAVP PLFGWSRYIP
+EGMQCSCGVD YYTLKPEVNN ESFVIYMFVV HFLIPLIIIS FCYGRLVCTV KEAAAQQQES
+ATTQKAEKEV TRMVIIMVIF FLICWVPYAY VAFYIFTHQG SEFGPIFMTV PAFFAKSSAI
+YNPVIYIMLN KQFRNCMITT LCCGKNPFGD DDASSAATSK TEATSVSTSQ VSPA*
+
+>P1;I51200
+rhodopsin - African clawed frog
+MNGTEGPNFY VPMSNKTGVV RSPFDYPQYY LAEPWQYSAL AAYMFLLILL GLPINFMTLF
+VTIQHKKLRT PLNYILLNLV FANHFMVLCG FTVTMYTSMH GYFIFGPTGC YIEGFFATLG
+GEVALWSLVV LAVERYIVVC KPMANFRFGE NHAIMGVAFT WIMALSCAAP PLFGWSRYIP
+EGMQCSCGVD YYTLKPEVNN ESFVIYMFIV HFTIPLIVIF FCYGRLLCTV KEAAAQQQES
+LTTQKAEKEV TRMVVIMVVF FLICWVPYAY VAFYIFTHQG SNFGPVFMTV PAFFAKSSAI
+YNPVIYIVLN KQFRNCLITT LCCGKNPFGD EDGSSAATSK TEASSVSSSQ VSPA*
+
+>P1;JN0120
+rhodopsin - Japanese lamprey
+MNGTEGDNFY VPFSNKTGLA RSPYEYPQYY LAEPWKYSAL AAYMFFLILV GFPVNFLTLF
+VTVQHKKLRT PLNYILLNLA MANLFMVLFG FTVTMYTSMN GYFVFGPTMC SIEGFFATLG
+GEVALWSLVV LAIERYIVIC KPMGNFRFGN THAIMGVAFT WIMALACAAP PLVGWSRYIP
+EGMQCSCGPD YYTLNPNFNN ESYVVYMFVV HFLVPFVIIF FCYGRLLCTV KEAAAAQQES
+ASTQKAEKEV TRMVVLMVIG FLVCWVPYAS VAFYIFTHQG SDFGATFMTL PAFFAKSSAL
+YNPVIYILMN KQFRNCMITT LCCGKNPLGD DE-SGASTSKT EVSSVSTSPV SPA*
+
+
+As with the FASTA format, each record starts with a line begining with ">"
+character. There is then a two letter sequence type (P1, F1, DL, DC, RL,
+RC, or XX), a semi colon, and the identification code. The second like is
+free text description. The remaining lines contain the sequence itself,
+terminating in an asterisk. Space separated blocks of ten letters as shown
+above are typical.
+
+Sequence codes and their meanings:
+
+P1 - Protein (complete)
+F1 - Protein (fragment)
+D1 - DNA (e.g. EMBOSS seqret output)
+DL - DNA (linear)
+DC - DNA (circular)
+RL - RNA (linear)
+RC - RNA (circular)
+N3 - tRNA
+N1 - Other functional RNA
+XX - Unknown
+"""
+
+from Bio.Alphabet import single_letter_alphabet, generic_protein, generic_dna, generic_rna
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+_pir_alphabets = {"P1" : generic_protein,
+ "F1" : generic_protein,
+ "D1" : generic_dna,
+ "DL" : generic_dna,
+ "DC" : generic_dna,
+ "RL" : generic_rna,
+ "RC" : generic_rna,
+ "N3" : generic_rna,
+ "XX" : single_letter_alphabet,
+ }
+
+#This is a generator function!
+def PirIterator(handle) :
+ """Generator function to iterate over Fasta records (as SeqRecord objects).
+
+ handle - input file
+ alphabet - optional alphabet
+ title2ids - A function that, when given the title of the FASTA
+ file (without the beginning >), will return the id, name and
+ description (in that order) for the record as a tuple of strings.
+
+ If this is not given, then the entire title line will be used
+ as the description, and the first word as the id and name.
+
+ Note that use of title2ids matches that of Bio.Fasta.SequenceParser
+ but the defaults are slightly different.
+ """
+ #Skip any text before the first record (e.g. blank lines, comments)
+ while True :
+ line = handle.readline()
+ if line == "" : return #Premature end of file, or just empty?
+ if line[0] == ">" :
+ break
+
+ while True :
+ if line[0]!=">" :
+ raise ValueError("Records in PIR files should start with '>' character")
+ pir_type = line[1:3]
+ if pir_type not in _pir_alphabets or line[3] != ";" :
+ raise ValueError("Records should start with '>XX;' where XX is a valid sequence type")
+ identifier = line[4:].strip()
+ description = handle.readline().strip()
+
+
+ lines = []
+ line = handle.readline()
+ while True:
+ if not line : break
+ if line[0] == ">": break
+ #Remove trailing whitespace, and any internal spaces
+ lines.append(line.rstrip().replace(" ",""))
+ line = handle.readline()
+ seq = "".join(lines)
+ if seq[-1] != "*" :
+ #Note the * terminator is present on nucleotide sequences too,
+ #it is not a stop codon!
+ raise ValueError("Sequences in PIR files should include a * terminator!")
+
+ #Return the record and then continue...
+ record = SeqRecord(Seq(seq[:-1], _pir_alphabets[pir_type]),
+ id = identifier, name = identifier,
+ description = description)
+ record.annotations["PIR-type"] = pir_type
+ yield record
+
+ if not line : return #StopIteration
+ assert False, "Should not reach this line"
+
+if __name__ == "__main__" :
+ print "Running quick self test"
+
+ from StringIO import StringIO
+ import os
+
+ for name in ["clustalw", "DMA_nuc", "DMB_prot", "B_nuc", "Cw_prot"] :
+ print name
+ filename = "../../Tests/NBRF/%s.pir" % name
+ if not os.path.isfile(filename) :
+ print "Missing %s" % filename
+ continue
+
+ records = list(PirIterator(open(filename)))
+ count = 0
+ for record in records :
+ count += 1
+ parts = record.description.split()
+ if "bases," in parts :
+ assert len(record) == int(parts[parts.index("bases,")-1])
+ print "Could read %s (%i records)" % (name, count)
+
--- /dev/null
+# Copyright 2009 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+#
+# This module is for reading and writing FASTQ and QUAL format files as
+# SeqRecord objects, and is expected to be used via the Bio.SeqIO API.
+
+"""Bio.SeqIO support for the "fastq" and "qual" file formats.
+
+Note that you are expected to use this code via the Bio.SeqIO interface, as
+shown below.
+
+The FASTQ file format is used frequently at the Wellcome Trust Sanger Institute
+to bundle a FASTA sequence and its PHRED quality data (integers between 0 and
+90). Rather than using a single FASTQ file, often paired FASTA and QUAL files
+are used containing the sequence and the quality information separately.
+
+The PHRED software reads DNA sequencing trace files, calls bases, and
+assigns a quality value between 0 and 90 to each called base using a logged
+transformation of the error probability, Q = -10 log10( Pe ), for example::
+
+ Pe = 0.0, Q = 0
+ Pe = 0.1, Q = 10
+ Pe = 0.01, Q = 20
+ ...
+ Pe = 0.00000001, Q = 80
+ Pe = 0.000000001, Q = 90
+
+In the QUAL format these quality values are held as space separated text in
+a FASTA like file format. In the FASTQ format, each quality values is encoded
+with a single ASCI character using chr(Q+33), meaning zero maps to the
+character "!" and for example 80 maps to "q". The sequences and quality are
+then stored in pairs in a FASTA like format.
+
+Unfortunately there is no official document describing the FASTQ file format,
+and worse, several related but different variants exist. Reasonable
+documentation exists at: http://maq.sourceforge.net/fastq.shtml
+
+Solexa/Illumina quality scores use Q = - 10 log10 ( Pe / (1-Pe) ), which can
+be negative or easily exceed 90. PHRED scores and Solexa scores are NOT
+interchangeable (but a reasonable mapping can be achieved between them).
+Confusingly Solexa produces a FASTQ like file but using their own score
+mapping instead.
+
+Also note that Roche 454 sequencers can output files in the QUAL format, and
+thankfully they use PHREP style scores like Sanger. To extract QUAL files from
+a Roche 454 SFF binary file, use the Roche off instrument command line tool
+"sffinfo" with the -q or -qual argument. You can extract a matching FASTA file
+using the -s or -seq argument instead.
+
+You are expected to use this module via the Bio.SeqIO functions, with the
+following format names:
+ - "fastq" means Sanger style FASTQ files using PHRED scores.
+ - "fastq-solexa" means Solexa/Illumina style FASTQ files.
+ - "qual" means simple quality files using PHRED scores.
+
+For example, consider the following short FASTQ file (extracted from a real
+NCBI dataset)::
+
+ @EAS54_6_R1_2_1_413_324
+ CCCTTCTTGTCTTCAGCGTTTCTCC
+ +
+ ;;3;;;;;;;;;;;;7;;;;;;;88
+ @EAS54_6_R1_2_1_540_792
+ TTGGCAGGCCAAGGCCGATGGATCA
+ +
+ ;;;;;;;;;;;7;;;;;-;;;3;83
+ @EAS54_6_R1_2_1_443_348
+ GTTGCTTCTGGCGTGGGTGGGGGGG
+ +
+ ;;;;;;;;;;;9;7;;.7;393333
+
+This contains three reads of length 25. From the read length these were
+probably originally from an early Solexa/Illumina sequencer but NCBI have
+followed the Sanger FASTQ convention and this actually uses PHRED style
+qualities. This means we can parse this file using Bio.SeqIO using "fastq"
+as the format name:
+
+ >>> from Bio import SeqIO
+ >>> for record in SeqIO.parse(open("Quality/example.fastq"), "fastq") :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
+ EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
+ EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
+
+The qualities are held as a list of integers in each record's annotation:
+
+ >>> print record
+ ID: EAS54_6_R1_2_1_443_348
+ Name: EAS54_6_R1_2_1_443_348
+ Description: EAS54_6_R1_2_1_443_348
+ Number of features: 0
+ Per letter annotation for: phred_quality
+ Seq('GTTGCTTCTGGCGTGGGTGGGGGGG', SingleLetterAlphabet())
+ >>> print record.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
+
+You can use the SeqRecord format method you can show this in the QUAL format:
+
+ >>> print record.format("qual")
+ >EAS54_6_R1_2_1_443_348
+ 26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
+ 24 18 18 18 18
+ <BLANKLINE>
+
+Or go back to the FASTQ format,
+
+ >>> print record.format("fastq")
+ @EAS54_6_R1_2_1_443_348
+ GTTGCTTCTGGCGTGGGTGGGGGGG
+ +
+ ;;;;;;;;;;;9;7;;.7;393333
+ <BLANKLINE>
+
+You can also get Biopython to convert the scores and show a Solexa style
+FASTQ file:
+
+ >>> print record.format("fastq-solexa")
+ @EAS54_6_R1_2_1_443_348
+ GTTGCTTCTGGCGTGGGTGGGGGGG
+ +
+ ZZZZZZZZZZZXZVZZMVZRXRRRR
+ <BLANKLINE>
+
+If you wanted to trim your sequences (perhaps to remove low quality regions,
+or to remove a primer sequence), try slicing the SeqRecord objects. e.g.
+
+ >>> sub_rec = record[5:15]
+ >>> print sub_rec
+ ID: EAS54_6_R1_2_1_443_348
+ Name: EAS54_6_R1_2_1_443_348
+ Description: EAS54_6_R1_2_1_443_348
+ Number of features: 0
+ Per letter annotation for: phred_quality
+ Seq('TTCTGGCGTG', SingleLetterAlphabet())
+ >>> print sub_rec.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 24, 26, 22, 26]
+ >>> print sub_rec.format("fastq")
+ @EAS54_6_R1_2_1_443_348
+ TTCTGGCGTG
+ +
+ ;;;;;;9;7;
+ <BLANKLINE>
+
+If you wanted to, you could read in this FASTQ file, and save it as a QUAL file:
+
+ >>> from Bio import SeqIO
+ >>> record_iterator = SeqIO.parse(open("Quality/example.fastq"), "fastq")
+ >>> out_handle = open("Quality/temp.qual", "w")
+ >>> SeqIO.write(record_iterator, out_handle, "qual")
+ 3
+ >>> out_handle.close()
+
+You can of course read in a QUAL file, such as the one we just created:
+
+ >>> from Bio import SeqIO
+ >>> for record in SeqIO.parse(open("Quality/temp.qual"), "qual") :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 ?????????????????????????
+ EAS54_6_R1_2_1_540_792 ?????????????????????????
+ EAS54_6_R1_2_1_443_348 ?????????????????????????
+
+Notice that QUAL files don't have a proper sequence present! But the quality
+information is there:
+
+ >>> print record
+ ID: EAS54_6_R1_2_1_443_348
+ Name: EAS54_6_R1_2_1_443_348
+ Description: EAS54_6_R1_2_1_443_348
+ Number of features: 0
+ Per letter annotation for: phred_quality
+ UnknownSeq(25, alphabet = SingleLetterAlphabet(), character = '?')
+ >>> print record.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
+
+Just to keep things tidy, if you are following this example yourself, you can
+delete this temporary file now:
+
+ >>> import os
+ >>> os.remove("Quality/temp.qual")
+
+Sometimes you won't have a FASTQ file, but rather just a pair of FASTA and QUAL
+files. Because the Bio.SeqIO system is designed for reading single files, you
+would have to read the two in separately and then combine the data. However,
+since this is such a common thing to want to do, there is a helper iterator
+defined in this module that does this for you - PairedFastaQualIterator.
+
+Alternatively, if you have enough RAM to hold all the records in memory at once,
+then a simple dictionary approach would work:
+
+ >>> from Bio import SeqIO
+ >>> reads = SeqIO.to_dict(SeqIO.parse(open("Quality/example.fasta"), "fasta"))
+ >>> for rec in SeqIO.parse(open("Quality/example.qual"), "qual") :
+ ... reads[rec.id].letter_annotations["phred_quality"]=rec.letter_annotations["phred_quality"]
+
+You can then access any record by its key, and get both the sequence and the
+quality scores.
+
+ >>> print reads["EAS54_6_R1_2_1_540_792"].format("fastq")
+ @EAS54_6_R1_2_1_540_792
+ TTGGCAGGCCAAGGCCGATGGATCA
+ +
+ ;;;;;;;;;;;7;;;;;-;;;3;83
+ <BLANKLINE>
+
+It is important that you explicitly tell Bio.SeqIO which FASTQ variant you are
+using ("fastq" for the Sanger standard using PHRED values, or "fastq-solexa"
+for the Solexa/Illumina variant), as this cannot be detected reliably
+automatically.
+"""
+__docformat__ = "epytext en" #Don't just use plain text in epydoc API pages!
+
+#See also http://blog.malde.org/index.php/2008/09/09/the-fastq-file-format-for-sequences/
+
+from Bio.Alphabet import single_letter_alphabet
+from Bio.Seq import Seq, UnknownSeq
+from Bio.SeqRecord import SeqRecord
+from Interfaces import SequentialSequenceWriter
+from math import log
+
+# define score offsets. See discussion for differences between Sanger and
+# Solexa offsets.
+SANGER_SCORE_OFFSET = 33
+SOLEXA_SCORE_OFFSET = 64
+
+def solexa_quality_from_phred(phred_quality) :
+ """Covert a PHRED quality (range 0 to about 90) to a Solexa quality.
+
+ This will return a floating point number, it is up to you to round this to
+ the nearest integer if appropriate. e.g.
+
+ >>> print "%0.2f" % round(solexa_quality_from_phred(80),2)
+ 80.00
+ >>> print "%0.2f" % round(solexa_quality_from_phred(50),2)
+ 50.00
+ >>> print "%0.2f" % round(solexa_quality_from_phred(20),2)
+ 19.96
+ >>> print "%0.2f" % round(solexa_quality_from_phred(10),2)
+ 9.54
+ >>> print "%0.2f" % round(solexa_quality_from_phred(1),2)
+ -5.87
+ """
+ return 10*log(10**(phred_quality/10.0) - 1, 10)
+
+def phred_quality_from_solexa(solexa_quality) :
+ """Convert a Solexa quality (which can be negative) to a PHRED quality.
+
+ This will return a floating point number, it is up to you to round this to
+ the nearest integer if appropriate. e.g.
+
+ >>> print "%0.2f" % round(phred_quality_from_solexa(80),2)
+ 80.00
+ >>> print "%0.2f" % round(phred_quality_from_solexa(20),2)
+ 20.04
+ >>> print "%0.2f" % round(phred_quality_from_solexa(10),2)
+ 10.41
+ >>> print "%0.2f" % round(phred_quality_from_solexa(0),2)
+ 3.01
+ >>> print "%0.2f" % round(phred_quality_from_solexa(-10),2)
+ 0.41
+ """
+ return 10*log(10**(solexa_quality/10.0) + 1, 10)
+
+def _get_phred_quality(record) :
+ """Extract PHRED qualities from a SeqRecord's letter_annotations (PRIVATE).
+
+ If there are no PHRED qualities, but there are Solexa qualities, those are
+ used instead after conversion.
+ """
+ try :
+ return record.letter_annotations["phred_quality"]
+ except KeyError :
+ pass
+ try :
+ return [phred_quality_from_solexa(q) for \
+ q in record.letter_annotations["solexa_quality"]]
+ except KeyError :
+ raise ValueError("No suitable quality scores found in letter_annotations "
+ "of SeqRecord (id=%s)." % record.id)
+
+def _get_solexa_quality(record) :
+ """Extract Solexa qualities from a SeqRecord's letter_annotations (PRIVATE).
+
+ If there are no Solexa qualities, but there are PHRED qualities, those are
+ used instead after conversion.
+ """
+ try :
+ return record.letter_annotations["solexa_quality"]
+ except KeyError :
+ pass
+ try :
+ return [solexa_quality_from_phred(q) for \
+ q in record.letter_annotations["phred_quality"]]
+ except KeyError :
+ raise ValueError("No suitable quality scores found in letter_annotation "
+ "of SeqRecord (id=%s)." % record.id)
+
+
+#TODO - Default to nucleotide or even DNA?
+def FastqGeneralIterator(handle) :
+ """Iterate over Fastq records as string tuples (not as SeqRecord objects).
+
+ This code does not try to interpret the quality string numerically. It
+ just returns tuples of the title, sequence and quality as strings. For
+ the sequence and quality, any whitespace (such as new lines) is removed.
+
+ Our SeqRecord based FASTQ iterators call this function internally, and then
+ turn the strings into a SeqRecord objects, mapping the quality string into
+ a list of numerical scores. If you want to do a custom quality mapping,
+ then you might consider calling this function directly.
+
+ For parsing FASTQ files, the title string from the "@" line at the start
+ of each record can optionally be omitted on the "+" lines. If it is
+ repeated, it must be identical.
+
+ The sequence string and the quality string can optionally be split over
+ multiple lines, although several sources discourage this. In comparison,
+ for the FASTA file format line breaks between 60 and 80 characters are
+ the norm.
+
+ WARNING - Because the "@" character can appear in the quality string,
+ this can cause problems as this is also the marker for the start of
+ a new sequence. In fact, the "+" sign can also appear as well. Some
+ sources recommended having no line breaks in the quality to avoid this,
+ but even that is not enough, consider this example::
+
+ @071113_EAS56_0053:1:1:998:236
+ TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA
+ +071113_EAS56_0053:1:1:998:236
+ IIIIIIIIIIIIIIIIIIIIIIIIIIIIICII+III
+ @071113_EAS56_0053:1:1:182:712
+ ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG
+ +
+ @IIIIIIIIIIIIIIICDIIIII<%<6&-*).(*%+
+ @071113_EAS56_0053:1:1:153:10
+ TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT
+ +
+ IIIIIIIIIIIICIIGIIIII>IAIIIE65I=II:6
+ @071113_EAS56_0053:1:3:990:501
+ TGGGAGGTTTTATGTGGA
+ AAGCAGCAATGTACAAGA
+ +
+ IIIIIII.IIIIII1@44
+ @-7.%<&+/$/%4(++(%
+
+ This is four PHRED encoded FASTQ entries originally from an NCBI source
+ (given the read length of 36, these are probably Solexa Illumna reads where
+ the quality has been mapped onto the PHRED values).
+
+ This example has been edited to illustrate some of the nasty things allowed
+ in the FASTQ format. Firstly, on the "+" lines most but not all of the
+ (redundant) identifiers are ommited. In real files it is likely that all or
+ none of these extra identifiers will be present.
+
+ Secondly, while the first three sequences have been shown without line
+ breaks, the last has been split over multiple lines. In real files any line
+ breaks are likely to be consistent.
+
+ Thirdly, some of the quality string lines start with an "@" character. For
+ the second record this is unavoidable. However for the fourth sequence this
+ only happens because its quality string is split over two lines. A naive
+ parser could wrongly treat any line starting with an "@" as the beginning of
+ a new sequence! This code copes with this possible ambiguity by keeping track
+ of the length of the sequence which gives the expected length of the quality
+ string.
+
+ Using this tricky example file as input, this short bit of code demonstrates
+ what this parsing function would return:
+
+ >>> handle = open("Quality/tricky.fastq", "rU")
+ >>> for (title, sequence, quality) in FastqGeneralIterator(handle) :
+ ... print title
+ ... print sequence, quality
+ 071113_EAS56_0053:1:1:998:236
+ TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIICII+III
+ 071113_EAS56_0053:1:1:182:712
+ ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG @IIIIIIIIIIIIIIICDIIIII<%<6&-*).(*%+
+ 071113_EAS56_0053:1:1:153:10
+ TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT IIIIIIIIIIIICIIGIIIII>IAIIIE65I=II:6
+ 071113_EAS56_0053:1:3:990:501
+ TGGGAGGTTTTATGTGGAAAGCAGCAATGTACAAGA IIIIIII.IIIIII1@44@-7.%<&+/$/%4(++(%
+ >>> handle.close()
+
+ Finally we note that some sources state that the quality string should
+ start with "!" (which using the PHRED mapping means the first letter always
+ has a quality score of zero). This rather restrictive rule is not widely
+ observed, so is therefore ignored here. One plus point about this "!" rule
+ is that (provided there are no line breaks in the quality sequence) it
+ would prevent the above problem with the "@" character.
+ """
+ #Skip any text before the first record (e.g. blank lines, comments?)
+ while True :
+ line = handle.readline()
+ if line == "" : return #Premature end of file, or just empty?
+ if line[0] == "@" :
+ break
+
+ while True :
+ if line[0]!="@" :
+ raise ValueError("Records in Fastq files should start with '@' character")
+ title_line = line[1:].rstrip()
+
+ seq_lines = []
+ line = handle.readline()
+ while True:
+ if not line :
+ raise ValueError("End of file without quality information.")
+ if line[0] == "+":
+ #The title here is optional, but if present must match!
+ if line[1:].rstrip() and line[1:].rstrip() != title_line :
+ raise ValueError("Sequence and quality captions differ.")
+ break
+ seq_lines.extend(line.split()) #removes any whitespace
+ line = handle.readline()
+
+ seq_string = "".join(seq_lines)
+ del seq_lines
+
+ quality_lines = []
+ line = handle.readline()
+ while True:
+ if not line : break
+ if line[0] == "@":
+ #This COULD be the start of a new sequence. However, it MAY just
+ #be a line of quality data which starts with a "@" character. We
+ #should be able to check this by looking at the sequence length
+ #and the amount of quality data found so far.
+ if len("".join(quality_lines)) >= len(seq_string) :
+ #We expect it to be equal if this is the start of a new record.
+ #If the quality data is longer, we'll raise an error below.
+ break
+ #Continue - its just some (more) sequence data.
+
+ quality_lines.extend(line.split()) #removes any whitespace
+ line = handle.readline()
+
+ quality_string = "".join(quality_lines)
+ del quality_lines
+
+ if len(seq_string) != len(quality_string) :
+ raise ValueError("Lengths of sequence and quality values differs "
+ " for %s (%i and %i)." \
+ % (title_line, len(seq_string), len(quality_string)))
+
+ #Return the record and then continue...
+ yield (title_line, seq_string, quality_string)
+ if not line : return #StopIteration at end of file
+ assert False, "Should not reach this line"
+
+#This is a generator function!
+def FastqPhredIterator(handle, alphabet = single_letter_alphabet, title2ids = None) :
+ """Generator function to iterate over FASTQ records (as SeqRecord objects).
+
+ - handle - input file
+ - alphabet - optional alphabet
+ - title2ids - A function that, when given the title line from the FASTQ
+ file (without the beginning >), will return the id, name and
+ description (in that order) for the record as a tuple of
+ strings. If this is not given, then the entire title line
+ will be used as the description, and the first word as the
+ id and name.
+
+ Note that use of title2ids matches that of Bio.SeqIO.FastaIO.
+
+ For each sequence in a (Sanger style) FASTQ file there is a matching string
+ encoding the PHRED qualities (integers between 0 and about 90) using ASCII
+ values with an offset of 33.
+
+ For example, consider a file containing three short reads::
+
+ @EAS54_6_R1_2_1_413_324
+ CCCTTCTTGTCTTCAGCGTTTCTCC
+ +
+ ;;3;;;;;;;;;;;;7;;;;;;;88
+ @EAS54_6_R1_2_1_540_792
+ TTGGCAGGCCAAGGCCGATGGATCA
+ +
+ ;;;;;;;;;;;7;;;;;-;;;3;83
+ @EAS54_6_R1_2_1_443_348
+ GTTGCTTCTGGCGTGGGTGGGGGGG
+ +
+ ;;;;;;;;;;;9;7;;.7;393333
+
+ For each sequence (e.g. "CCCTTCTTGTCTTCAGCGTTTCTCC") there is a matching
+ string encoding the PHRED qualities using a ASCI values with an offset of
+ 33 (e.g. ";;3;;;;;;;;;;;;7;;;;;;;88").
+
+ Using this module directly you might run:
+
+ >>> handle = open("Quality/example.fastq", "rU")
+ >>> for record in FastqPhredIterator(handle) :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
+ EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
+ EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
+ >>> handle.close()
+
+ Typically however, you would call this via Bio.SeqIO instead with "fastq" as
+ the format:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Quality/example.fastq", "rU")
+ >>> for record in SeqIO.parse(handle, "fastq") :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
+ EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
+ EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
+ >>> handle.close()
+
+ If you want to look at the qualities, they are record in each record's
+ per-letter-annotation dictionary as a simple list of integers:
+
+ >>> print record.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
+ """
+ for title_line, seq_string, quality_string in FastqGeneralIterator(handle) :
+ if title2ids :
+ id, name, descr = title2ids(title_line)
+ else :
+ descr = title_line
+ id = descr.split()[0]
+ name = id
+ record = SeqRecord(Seq(seq_string, alphabet),
+ id=id, name=name, description=descr)
+
+ assert SANGER_SCORE_OFFSET == ord("!")
+ #According to BioPerl documentation at least, the first character should
+ #be an "!" (and therefore quality zero). This seems crazy - what if the
+ #sequence has been trimmed to remove any poor quality sequence? In any
+ #case real examples from the NCBI don't follow this practice, so we
+ #won't enforce it here.
+ #e.g. ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000271/fastq/200x36x36-071113_EAS56_0053-s_1_1.fastq.gz
+ #
+ #if quality_string[0] != "!" :
+ # raise ValueError("The quality string should always start with a ! character.")
+ qualities = [ord(letter)-SANGER_SCORE_OFFSET for letter in quality_string]
+ if qualities :
+ if min(qualities) < 0 or max(qualities) > 90 :
+ raise ValueError("Quality score outside 0 to 90 found - these are perhaps "
+ "in a Solexa/Illumina format, not the Sanger FASTQ format "
+ "which uses PHRED scores.")
+ record.letter_annotations["phred_quality"] = qualities
+ yield record
+
+#This is a generator function!
+def FastqSolexaIterator(handle, alphabet = single_letter_alphabet, title2ids = None) :
+ """Parsing the Solexa/Illumina FASTQ like files (which differ in the quality mapping).
+
+ The optional arguments are the same as those for the FastqPhredIterator.
+
+ For each sequence in Solexa/Illumina FASTQ files there is a matching string
+ encoding the Solexa integer qualities using ASCII values with an offset
+ of 64. Solexa scores are scaled differently to PHRED scores, and Biopython
+ will NOT perform any automatic conversion when loading.
+
+ For example, consider a file containing these five records::
+
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
+ GATGTGCAATACCTTTGTAGAGGAA
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
+ YYYYYYYYYYYYYYYYYYWYWYYSU
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
+ GGTTTGAGAAAGAGAAATGAGATAA
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
+ YYYYYYYYYWYYYYWWYYYWYWYWW
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
+ GAGGGTGTTGATCATGATGATGGCG
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
+ YYYYYYYYYYYYYWYYWYYSYYYSY
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
+ GGAAACAAAGTTTTTCTCAACATAG
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
+ YYYYYYYYYYYYYYYYYYWWWWYWY
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
+ GTATTATTTAATGGCATACACTCAA
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
+
+ Using this module directly you might run:
+
+ >>> handle = open("Quality/solexa_example.fastq", "rU")
+ >>> for record in FastqSolexaIterator(handle) :
+ ... print record.id, record.seq
+ SLXA-B3_649_FC8437_R1_1_1_610_79 GATGTGCAATACCTTTGTAGAGGAA
+ SLXA-B3_649_FC8437_R1_1_1_397_389 GGTTTGAGAAAGAGAAATGAGATAA
+ SLXA-B3_649_FC8437_R1_1_1_850_123 GAGGGTGTTGATCATGATGATGGCG
+ SLXA-B3_649_FC8437_R1_1_1_362_549 GGAAACAAAGTTTTTCTCAACATAG
+ SLXA-B3_649_FC8437_R1_1_1_183_714 GTATTATTTAATGGCATACACTCAA
+ >>> handle.close()
+
+ Typically however, you would call this via Bio.SeqIO instead with "fastq" as
+ the format:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Quality/solexa_example.fastq", "rU")
+ >>> for record in SeqIO.parse(handle, "fastq-solexa") :
+ ... print record.id, record.seq
+ SLXA-B3_649_FC8437_R1_1_1_610_79 GATGTGCAATACCTTTGTAGAGGAA
+ SLXA-B3_649_FC8437_R1_1_1_397_389 GGTTTGAGAAAGAGAAATGAGATAA
+ SLXA-B3_649_FC8437_R1_1_1_850_123 GAGGGTGTTGATCATGATGATGGCG
+ SLXA-B3_649_FC8437_R1_1_1_362_549 GGAAACAAAGTTTTTCTCAACATAG
+ SLXA-B3_649_FC8437_R1_1_1_183_714 GTATTATTTAATGGCATACACTCAA
+ >>> handle.close()
+
+ If you want to look at the qualities, they are recorded in each record's
+ per-letter-annotation dictionary as a simple list of integers:
+
+ >>> print record.letter_annotations["solexa_quality"]
+ [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 25, 25, 25, 25, 23, 25, 23, 23, 21, 23, 23, 23, 17, 17]
+
+ These scores aren't very good, but they are high enough that they map
+ almost exactly onto PHRED scores:
+
+ >>> print "%0.2f" % phred_quality_from_solexa(25)
+ 25.01
+
+ Let's look at another example read which is even worse, where there are
+ more noticeable differences between the Solexa and PHRED scores::
+
+ @slxa_0013_1_0001_24
+ ACAAAAATCACAAGCATTCTTATACACC
+ +slxa_0013_1_0001_24
+ ??????????????????:??<?<-6%.
+
+ Again, you would typically use Bio.SeqIO to read this file in (rather than
+ calling the Bio.SeqIO.QualtityIO module directly). Most FASTQ files will
+ contain thousands of reads, so you would normally use Bio.SeqIO.parse()
+ as shown above. This example has only as one entry, so instead we can
+ use the Bio.SeqIO.read() function:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Quality/solexa.fastq", "rU")
+ >>> record = SeqIO.read(handle, "fastq-solexa")
+ >>> handle.close()
+ >>> print record.id, record.seq
+ slxa_0013_1_0001_24 ACAAAAATCACAAGCATTCTTATACACC
+ >>> print record.letter_annotations["solexa_quality"]
+ [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -6, -1, -1, -4, -1, -4, -19, -10, -27, -18]
+
+ These quality scores are so low that when converted from the Solexa scheme
+ into PHRED scores they look quite different:
+
+ >>> print "%0.2f" % phred_quality_from_solexa(-1)
+ 2.54
+
+ Note you can use the Bio.SeqIO.write() function or the SeqRecord's format
+ method to output the record(s):
+
+ >>> print record.format("fastq-solexa")
+ @slxa_0013_1_0001_24
+ ACAAAAATCACAAGCATTCTTATACACC
+ +
+ ??????????????????:??<?<-6%.
+ <BLANKLINE>
+
+ Note this output is slightly different from the input file as Biopython
+ has left out the optional repetition of the sequence identifier on the "+"
+ line. If you want the to use PHRED scores, use "fastq" or "qual" as the
+ output format instead, and Biopython will do the conversion for you:
+
+ >>> print record.format("fastq")
+ @slxa_0013_1_0001_24
+ ACAAAAATCACAAGCATTCTTATACACC
+ +
+ $$$$$$$$$$$$$$$$$$"$$"$"!!!!
+ <BLANKLINE>
+
+ >>> print record.format("qual")
+ >slxa_0013_1_0001_24
+ 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 3 3 1 3 1 0 0 0 0
+ <BLANKLINE>
+ """
+ for title_line, seq_string, quality_string in FastqGeneralIterator(handle) :
+ if title2ids :
+ id, name, descr = title_line
+ else :
+ descr = title_line
+ id = descr.split()[0]
+ name = id
+ record = SeqRecord(Seq(seq_string, alphabet),
+ id=id, name=name, description=descr)
+ qualities = [ord(letter)-SOLEXA_SCORE_OFFSET for letter in quality_string]
+ #DO NOT convert these into PHRED qualities automatically!
+ record.letter_annotations["solexa_quality"] = qualities
+ yield record
+
+def QualPhredIterator(handle, alphabet = single_letter_alphabet, title2ids = None) :
+ """For QUAL files which include PHRED quality scores, but no sequence.
+
+ For example, consider this short QUAL file::
+
+ >EAS54_6_R1_2_1_413_324
+ 26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26
+ 26 26 26 23 23
+ >EAS54_6_R1_2_1_540_792
+ 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26
+ 26 18 26 23 18
+ >EAS54_6_R1_2_1_443_348
+ 26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
+ 24 18 18 18 18
+
+ Using this module directly you might run:
+
+ >>> handle = open("Quality/example.qual", "rU")
+ >>> for record in QualPhredIterator(handle) :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 ?????????????????????????
+ EAS54_6_R1_2_1_540_792 ?????????????????????????
+ EAS54_6_R1_2_1_443_348 ?????????????????????????
+ >>> handle.close()
+
+ Typically however, you would call this via Bio.SeqIO instead with "qual"
+ as the format:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Quality/example.qual", "rU")
+ >>> for record in SeqIO.parse(handle, "qual") :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 ?????????????????????????
+ EAS54_6_R1_2_1_540_792 ?????????????????????????
+ EAS54_6_R1_2_1_443_348 ?????????????????????????
+ >>> handle.close()
+
+ Becase QUAL files don't contain the sequence string itself, the seq
+ property is set to an UnknownSeq object. As no alphabet was given, this
+ has defaulted to a generic single letter alphabet and the character "?"
+ used.
+
+ By specifying a nucleotide alphabet, "N" is used instead:
+
+ >>> from Bio import SeqIO
+ >>> from Bio.Alphabet import generic_dna
+ >>> handle = open("Quality/example.qual", "rU")
+ >>> for record in SeqIO.parse(handle, "qual", alphabet=generic_dna) :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 NNNNNNNNNNNNNNNNNNNNNNNNN
+ EAS54_6_R1_2_1_540_792 NNNNNNNNNNNNNNNNNNNNNNNNN
+ EAS54_6_R1_2_1_443_348 NNNNNNNNNNNNNNNNNNNNNNNNN
+ >>> handle.close()
+
+ However, the quality scores themselves are available as a list of integers
+ in each record's per-letter-annotation:
+
+ >>> print record.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
+
+ You can still slice one of these SeqRecord objects with an UnknownSeq:
+
+ >>> sub_record = record[5:10]
+ >>> print sub_record.id, sub_record.letter_annotations["phred_quality"]
+ EAS54_6_R1_2_1_443_348 [26, 26, 26, 26, 26]
+ """
+ #Skip any text before the first record (e.g. blank lines, comments)
+ while True :
+ line = handle.readline()
+ if line == "" : return #Premature end of file, or just empty?
+ if line[0] == ">" :
+ break
+
+ while True :
+ if line[0]!=">" :
+ raise ValueError("Records in Fasta files should start with '>' character")
+ if title2ids :
+ id, name, descr = title2ids(line[1:].rstrip())
+ else :
+ descr = line[1:].rstrip()
+ id = descr.split()[0]
+ name = id
+
+ qualities = []
+ line = handle.readline()
+ while True:
+ if not line : break
+ if line[0] == ">": break
+ qualities.extend([int(word) for word in line.split()])
+ line = handle.readline()
+
+ if qualities :
+ if min(qualities) < 0 or max(qualities) > 90 :
+ raise ValueError(("Quality score range for %s is %i to %i, outside the " \
+ +"expected 0 to 90. Perhaps these are Solexa/Illumina " \
+ +"scores, and not PHRED scores?") \
+ % (id, min(qualities), max(qualities)))
+
+ #Return the record and then continue...
+ record = SeqRecord(UnknownSeq(len(qualities), alphabet),
+ id = id, name = name, description = descr)
+ record.letter_annotations["phred_quality"] = qualities
+ yield record
+
+ if not line : return #StopIteration
+ assert False, "Should not reach this line"
+
+class FastqPhredWriter(SequentialSequenceWriter):
+ """Class to write FASTQ format files (using PHRED quality scores).
+
+ Although you can use this class directly, you are strongly encouraged
+ to use the Bio.SeqIO.write() function instead. For example, this code
+ reads in a FASTQ (PHRED) file and re-saves it as another FASTQ (PHRED)
+ file:
+
+ >>> from Bio import SeqIO
+ >>> record_iterator = SeqIO.parse(open("Quality/example.fastq"), "fastq")
+ >>> out_handle = open("Quality/temp.fastq", "w")
+ >>> SeqIO.write(record_iterator, out_handle, "fastq")
+ 3
+ >>> out_handle.close()
+
+ You might want to do this if the original file included extra line breaks,
+ which while valid may not be supported by all tools. The output file from
+ Biopython will have each sequence on a single line, and each quality
+ string on a single line (which is considered desirable for maximum
+ compatibility).
+
+ In this next example, a Solexa FASTQ file is converted into a standard
+ Sanger style FASTQ file using PHRED qualities:
+
+ >>> from Bio import SeqIO
+ >>> record_iterator = SeqIO.parse(open("Quality/solexa.fastq"), "fastq-solexa")
+ >>> out_handle = open("Quality/temp.fastq", "w")
+ >>> SeqIO.write(record_iterator, out_handle, "fastq")
+ 1
+ >>> out_handle.close()
+
+ This code is also called if you use the .format("fastq") method of a
+ SeqRecord.
+
+ P.S. To avoid cluttering up your working directory, you can delete this
+ temporary file now:
+
+ >>> import os
+ >>> os.remove("Quality/temp.fastq")
+
+ """
+ def write_record(self, record):
+ """Write a single FASTQ record to the file."""
+ assert self._header_written
+ assert not self._footer_written
+ self._record_written = True
+
+ #TODO - Is an empty sequence allowed in FASTQ format?
+ assert SANGER_SCORE_OFFSET == ord("!")
+ #This rounds to the nearest integer:
+ qualities = "".join([chr(int(round(q+SANGER_SCORE_OFFSET,0))) for q \
+ in _get_phred_quality(record)])
+ if record.seq is None:
+ raise ValueError("No sequence for record %s" % record.id)
+ if len(qualities) != len(record) :
+ raise ValueError("Record %s has sequence length %i but %i quality scores" \
+ % (record.id, len(record), len(qualities)))
+
+ title = self.clean(record.id) #TODO - add the description too? cf Fasta output
+ self.handle.write("@%s\n%s\n+\n%s\n" % (title, record.seq, qualities))
+
+class QualPhredWriter(SequentialSequenceWriter):
+ """Class to write QUAL format files (using PHRED quality scores).
+
+ Although you can use this class directly, you are strongly encouraged
+ to use the Bio.SeqIO.write() function instead. For example, this code
+ reads in a FASTQ file and saves the quality scores into a QUAL file:
+
+ >>> from Bio import SeqIO
+ >>> record_iterator = SeqIO.parse(open("Quality/example.fastq"), "fastq")
+ >>> out_handle = open("Quality/temp.qual", "w")
+ >>> SeqIO.write(record_iterator, out_handle, "qual")
+ 3
+ >>> out_handle.close()
+
+ This code is also called if you use the .format("qual") method of a
+ SeqRecord.
+
+ P.S. Don't forget to clean up the temp file if you don't need it anymore:
+
+ >>> import os
+ >>> os.remove("Quality/temp.qual")
+ """
+ def __init__(self, handle, wrap=60, record2title=None):
+ """Create a QUAL writer.
+
+ Arguments:
+ - handle - Handle to an output file, e.g. as returned
+ by open(filename, "w")
+ - wrap - Optional line length used to wrap sequence lines.
+ Defaults to wrapping the sequence at 60 characters
+ Use zero (or None) for no wrapping, giving a single
+ long line for the sequence.
+ - record2title - Optional function to return the text to be
+ used for the title line of each record. By default
+ a combination of the record.id and record.description
+ is used. If the record.description starts with the
+ record.id, then just the record.description is used.
+
+ The record2title argument is present for consistency with the
+ Bio.SeqIO.FastaIO writer class.
+ """
+ SequentialSequenceWriter.__init__(self, handle)
+ #self.handle = handle
+ self.wrap = None
+ if wrap :
+ if wrap < 1 :
+ raise ValueError
+ self.wrap = wrap
+ self.record2title = record2title
+
+ def write_record(self, record):
+ """Write a single QUAL record to the file."""
+ assert self._header_written
+ assert not self._footer_written
+ self._record_written = True
+
+ if self.record2title :
+ title=self.clean(self.record2title(record))
+ else :
+ id = self.clean(record.id)
+ description = self.clean(record.description)
+
+ #if description[:len(id)]==id :
+ if description and description.split(None,1)[0]==id :
+ #The description includes the id at the start
+ title = description
+ else :
+ title = "%s %s" % (id, description)
+
+ assert "\n" not in title
+ assert "\r" not in title
+ self.handle.write(">%s\n" % title)
+
+ #This rounds to the nearest integer.
+ #TODO - can we put a float in a qual file?
+ qualities = [("%i" % round(q,0)) for q in _get_phred_quality(record)]
+
+ if self.wrap :
+ while qualities :
+ line=qualities.pop(0)
+ while qualities \
+ and len(line) + 1 + len(qualities[0]) < self.wrap :
+ line += " " + qualities.pop(0)
+ self.handle.write(line + "\n")
+ else :
+ data = " ".join(qualities)
+ self.handle.write(data + "\n")
+
+class FastqSolexaWriter(SequentialSequenceWriter):
+ """Class to write FASTQ format files (using Solexa quality scores).
+
+ Although you can use this class directly, you are strongly encouraged
+ to use the Bio.SeqIO.write() function instead. For example, this code
+ reads in a FASTQ file and re-saves it as another FASTQ file:
+
+ >>> from Bio import SeqIO
+ >>> record_iterator = SeqIO.parse(open("Quality/solexa.fastq"), "fastq-solexa")
+ >>> out_handle = open("Quality/temp.fastq", "w")
+ >>> SeqIO.write(record_iterator, out_handle, "fastq-solexa")
+ 1
+ >>> out_handle.close()
+
+ You might want to do this if the original file included extra line
+ breaks, which (while valid) may not be supported by all tools. The
+ output file from Biopython will have each sequence on a single line, and
+ each quality string on a single line (which is considered desirable for
+ maximum compatibility).
+
+ This code is also called if you use the .format("fastq-solexa") method of
+ a SeqRecord.
+
+ P.S. Don't forget to delete the temp file if you don't need it anymore:
+
+ >>> import os
+ >>> os.remove("Quality/temp.fastq")
+ """
+ def write_record(self, record):
+ """Write a single FASTQ record to the file."""
+ assert self._header_written
+ assert not self._footer_written
+ self._record_written = True
+
+ #TODO - Is an empty sequence allowed in FASTQ format?
+ qualities = "".join([chr(int(round(q+SOLEXA_SCORE_OFFSET,0))) for q \
+ in _get_solexa_quality(record)])
+ if record.seq is None:
+ raise ValueError("No sequence for record %s" % record.id)
+ if len(qualities) != len(record) :
+ raise ValueError("Record %s has sequence length %i but %i quality scores" \
+ % (record.id, len(record), len(qualities)))
+
+ title = self.clean(record.id) #TODO - add the description too? cf Fasta output
+ self.handle.write("@%s\n%s\n+\n%s\n" % (title, record.seq, qualities))
+
+def PairedFastaQualIterator(fasta_handle, qual_handle, alphabet = single_letter_alphabet, title2ids = None) :
+ """Iterate over matched FASTA and QUAL files as SeqRecord objects.
+
+ For example, consider this short QUAL file::
+
+ >EAS54_6_R1_2_1_413_324
+ 26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26
+ 26 26 26 23 23
+ >EAS54_6_R1_2_1_540_792
+ 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26
+ 26 18 26 23 18
+ >EAS54_6_R1_2_1_443_348
+ 26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
+ 24 18 18 18 18
+
+ And a matching FASTA file::
+
+ >EAS54_6_R1_2_1_413_324
+ CCCTTCTTGTCTTCAGCGTTTCTCC
+ >EAS54_6_R1_2_1_540_792
+ TTGGCAGGCCAAGGCCGATGGATCA
+ >EAS54_6_R1_2_1_443_348
+ GTTGCTTCTGGCGTGGGTGGGGGGG
+
+ You can parse these separately using Bio.SeqIO with the "qual" and
+ "fasta" formats, but then you'll get a group of SeqRecord objects with
+ no sequence, and a matching group with the sequence but not the
+ qualities. Because it only deals with one input file handle, Bio.SeqIO
+ can't be used to read the two files together - but this function can!
+ For example,
+
+ >>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
+ ... open("Quality/example.qual", "rU"))
+ >>> for record in rec_iter :
+ ... print record.id, record.seq
+ EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
+ EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
+ EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
+
+ As with the FASTQ or QUAL parsers, if you want to look at the qualities,
+ they are in each record's per-letter-annotation dictionary as a simple
+ list of integers:
+
+ >>> print record.letter_annotations["phred_quality"]
+ [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
+
+ If you have access to data as a FASTQ format file, using that directly
+ would be simpler and more straight forward. Note that you can easily use
+ this function to convert paired FASTA and QUAL files into FASTQ files:
+
+ >>> from Bio import SeqIO
+ >>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
+ ... open("Quality/example.qual", "rU"))
+ >>> out_handle = open("Quality/temp.fastq", "w")
+ >>> SeqIO.write(rec_iter, out_handle, "fastq")
+ 3
+ >>> out_handle.close()
+
+ And don't forget to clean up the temp file if you don't need it anymore:
+
+ >>> import os
+ >>> os.remove("Quality/temp.fastq")
+ """
+ from Bio.SeqIO.FastaIO import FastaIterator
+ fasta_iter = FastaIterator(fasta_handle, alphabet=alphabet, \
+ title2ids=title2ids)
+ qual_iter = QualPhredIterator(qual_handle, alphabet=alphabet, \
+ title2ids=title2ids)
+
+ #Using zip(...) would create a list loading everything into memory!
+ #It would also not catch any extra records found in only one file.
+ while True :
+ try :
+ f_rec = fasta_iter.next()
+ except StopIteration :
+ f_rec = None
+ try :
+ q_rec = qual_iter.next()
+ except StopIteration :
+ q_rec = None
+ if f_rec is None and q_rec is None :
+ #End of both files
+ break
+ if f_rec is None :
+ raise ValueError("FASTA file has more entries than the QUAL file.")
+ if q_rec is None :
+ raise ValueError("QUAL file has more entries than the FASTA file.")
+ if f_rec.id != q_rec.id :
+ raise ValueError("FASTA and QUAL entries do not match (%s vs %s)." \
+ % (f_rec.id, q_rec.id))
+ if len(f_rec) != len(q_rec.letter_annotations["phred_quality"]) :
+ raise ValueError("Sequence length and number of quality scores disagree for %s" \
+ % f_rec.id)
+ #Merge the data....
+ f_rec.letter_annotations["phred_quality"] = q_rec.letter_annotations["phred_quality"]
+ yield f_rec
+ #Done
+
+
+def _test():
+ """Run the Bio.SeqIO module's doctests.
+
+ This will try and locate the unit tests directory, and run the doctests
+ from there in order that the relative paths used in the examples work.
+ """
+ import doctest
+ import os
+ if os.path.isdir(os.path.join("..","..","Tests")) :
+ print "Runing doctests..."
+ cur_dir = os.path.abspath(os.curdir)
+ os.chdir(os.path.join("..","..","Tests"))
+ assert os.path.isfile("Quality/example.fastq")
+ assert os.path.isfile("Quality/example.fasta")
+ assert os.path.isfile("Quality/example.qual")
+ assert os.path.isfile("Quality/tricky.fastq")
+ assert os.path.isfile("Quality/solexa.fastq")
+ doctest.testmod()
+ os.chdir(cur_dir)
+ del cur_dir
+ print "Done"
+
+if __name__ == "__main__" :
+ _test()
+
--- /dev/null
+# Copyright 2006 by Peter Cock. All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format.
+
+You are expected to use this module via the Bio.SeqIO functions.
+See also the Bio.SwissProt module which offers more than just accessing
+the sequences as SeqRecord objects."""
+
+from Bio.SwissProt import SProt
+import cStringIO
+
+#This is a generator function!
+def SwissIterator(handle) :
+ """Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.
+
+ Every section from the ID line to the terminating // becomes
+ a single SeqRecord with associated annotation and features.
+
+ This parser is for the flat file "swiss" format as used by:
+ * Swiss-Prot aka SwissProt
+ * TrEMBL
+ * UniProtKB aka UniProt Knowledgebase
+
+ It does NOT read their new XML file format.
+ http://www.expasy.org/sprot/
+
+ For consistency with BioPerl and EMBOSS we call this the "swiss"
+ format.
+ """
+ parser = SProt.SequenceParser()
+ lines = []
+ for line in handle:
+ lines.append(line)
+ if line[:2]=='//':
+ handle = cStringIO.StringIO("".join(lines))
+ record = parser.parse(handle)
+ lines = []
+ yield record
+ #If there are more lines, it could only be a partial record.
+ #Should we try and parse them anyway?
+
+
+if __name__ == "__main__" :
+ print "Quick self test..."
+
+ example_filename = "../../Tests/SwissProt/sp008"
+
+ import os
+ if not os.path.isfile(example_filename):
+ print "Missing test file %s" % example_filename
+ else :
+ #Try parsing it!
+ handle = open(example_filename)
+ records = SwissIterator(handle)
+ for record in records:
+ print record.name
+ print record.id
+ print record.annotations['keywords']
+ print repr(record.annotations['organism'])
+ print record.seq.tostring()[:20] + "..."
+ handle.close()
--- /dev/null
+# Copyright 2008 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Bio.SeqIO support for the "tab" (simple tab separated) file format.
+
+You are expected to use this module via the Bio.SeqIO functions.
+
+The "tab" format is an ad-hoc plain text file format where each sequence is
+on one (long) line. Each line contains the identifier/description, followed
+by a tab, followed by the sequence. For example, consider the following
+short FASTA format file:
+
+>ID123456 possible binding site?
+CATCNAGATGACACTACGACTACGACTCAGACTAC
+>ID123457 random sequence
+ACACTACGACTACGACTCAGACTACAAN
+
+Apart from the descriptions, this can be represented in the simple two column
+tab separated format as follows:
+
+ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC
+ID123457(tab)ACACTACGACTACGACTCAGACTACAAN
+
+When reading this file, "ID123456" or "ID123457" will be taken as the record's
+.id and .name property. There is no other information to record.
+
+Similarly, when writing to this format, Biopython will ONLY record the record's
+.id and .seq (and not the description or any other information) as in the example
+above.
+"""
+
+from Bio.Alphabet import single_letter_alphabet
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Interfaces import SequentialSequenceWriter
+
+#This is a generator function!
+def TabIterator(handle, alphabet = single_letter_alphabet) :
+ """Iterates over tab separated lines (as SeqRecord objects).
+
+ Each line of the file should contain one tab only, dividing the line
+ into an identifier and the full sequence.
+
+ handle - input file
+ alphabet - optional alphabet
+
+ The first field is taken as the record's .id and .name (regardless of
+ any spaces within the text) and the second field is the sequence.
+
+ Any blank lines are ignored.
+ """
+ for line in handle :
+ try :
+ title, seq = line.split("\t") #will fail if more than one tab!
+ except :
+ if line.strip() == "" :
+ #It's a blank line, ignore it
+ continue
+ raise ValueError("Each line should have one tab separating the" + \
+ " title and sequence, this line has %i tabs: %s" \
+ % (line.count("\t"), repr(line)))
+ title = title.strip()
+ seq = seq.strip() #removes the trailing new line
+ yield SeqRecord(Seq(seq, alphabet), id = title, name = title)
+
+class TabWriter(SequentialSequenceWriter):
+ """Class to write simple tab separated format files.
+
+ Each line consists of "id(tab)sequence" only.
+
+ Any description, name or other annotation is not recorded.
+ """
+ def write_record(self, record):
+ """Write a single tab line to the file."""
+ assert self._header_written
+ assert not self._footer_written
+ self._record_written = True
+
+ title = self.clean(record.id)
+ seq = self._get_seq_string(record) #Catches sequence being None
+ assert "\t" not in title
+ assert "\n" not in title
+ assert "\r" not in title
+ assert "\t" not in seq
+ assert "\n" not in seq
+ assert "\r" not in seq
+ self.handle.write("%s\t%s\n" % (title, seq))
+
+
+if __name__ == "__main__" :
+ print "Running quick self test"
+ from StringIO import StringIO
+
+ #This example has a trailing blank line which should be ignored
+ handle = StringIO("Alpha\tAAAAAAA\nBeta\tCCCCCCC\n\n")
+ records = list(TabIterator(handle))
+ assert len(records) == 2
+
+ handle = StringIO("Alpha\tAAAAAAA\tExtra\nBeta\tCCCCCCC\n")
+ try :
+ records = list(TabIterator(handle))
+ assert False, "Should have reject this invalid example!"
+ except ValueError :
+ #Good!
+ pass
+
+ print "Done"
--- /dev/null
+# Copyright 2006-2008 by Peter Cock. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+#
+#Nice link:
+# http://www.ebi.ac.uk/help/formats_frame.html
+
+"""Sequence input/output as SeqRecord objects.
+
+Bio.SeqIO is also documented at U{http://biopython.org/wiki/SeqIO} and by
+a whole chapter in our tutorial:
+ - U{http://biopython.org/DIST/docs/tutorial/Tutorial.html}
+ - U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf}
+
+Input
+=====
+The main function is Bio.SeqIO.parse(...) which takes an input file handle,
+and format string. This returns an iterator giving SeqRecord objects:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Fasta/f002", "rU")
+ >>> for record in SeqIO.parse(handle, "fasta") :
+ ... print record.id, len(record)
+ gi|1348912|gb|G26680|G26680 633
+ gi|1348917|gb|G26685|G26685 413
+ gi|1592936|gb|G29385|G29385 471
+ >>> handle.close()
+
+Note that the parse() function will all invoke the relevant parser for the
+format with its default settings. You may want more control, in which case
+you need to create a format specific sequence iterator directly.
+
+For non-interlaced files (e.g. Fasta, GenBank, EMBL) with multiple records
+using a sequence iterator can save you a lot of memory (RAM). There is
+less benefit for interlaced file formats (e.g. most multiple alignment file
+formats). However, an iterator only lets you access the records one by one.
+
+If you want random access to the records by number, turn this into a list:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Fasta/f002", "rU")
+ >>> records = list(SeqIO.parse(handle, "fasta"))
+ >>> handle.close()
+ >>> print records[1].id
+ gi|1348917|gb|G26685|G26685
+
+If you want random access to the records by a key such as the record id,
+turn the iterator into a dictionary:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Fasta/f002", "rU")
+ >>> record_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
+ >>> handle.close()
+ >>> print len(record_dict["gi|1348917|gb|G26685|G26685"])
+ 413
+
+If you expect your file to contain one-and-only-one record, then we provide
+the following 'helper' function which will return a single SeqRecord, or
+raise an exception if there are no records or more than one record:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Fasta/f001", "rU")
+ >>> record = SeqIO.read(handle, "fasta")
+ >>> handle.close()
+ >>> print record.id, len(record)
+ gi|3318709|pdb|1A91| 79
+
+This style is useful when you expect a single record only (and would
+consider multiple records an error). For example, when dealing with GenBank
+files for bacterial genomes or chromosomes, there is normally only a single
+record. Alternatively, use this with a handle when download a single record
+from the internet.
+
+However, if you just want the first record from a file containing multiple
+record, use the iterator's next() method:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Fasta/f002", "rU")
+ >>> record = SeqIO.parse(handle, "fasta").next()
+ >>> handle.close()
+ >>> print record.id, len(record)
+ gi|1348912|gb|G26680|G26680 633
+
+The above code will work as long as the file contains at least one record.
+Note that if there is more than one record, the remaining records will be
+silently ignored.
+
+Input - Alignments
+==================
+You can read in alignment files as Alignment objects using Bio.AlignIO.
+Alternatively, reading in an alignment file format via Bio.SeqIO will give
+you a SeqRecord for each row of each alignment:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Clustalw/hedgehog.aln", "rU")
+ >>> for record in SeqIO.parse(handle, "clustal") :
+ ... print record.id, len(record)
+ gi|167877390|gb|EDS40773.1| 447
+ gi|167234445|ref|NP_001107837. 447
+ gi|74100009|gb|AAZ99217.1| 447
+ gi|13990994|dbj|BAA33523.2| 447
+ gi|56122354|gb|AAV74328.1| 447
+ >>> handle.close()
+
+Output
+======
+Use the function Bio.SeqIO.write(...), which takes a complete set of
+SeqRecord objects (either as a list, or an iterator), an output file handle
+and of course the file format::
+
+ from Bio import SeqIO
+ records = ...
+ handle = open("example.faa", "w")
+ SeqIO.write(records, handle, "fasta")
+ handle.close()
+
+In general, you are expected to call this function once (with all your
+records) and then close the file handle.
+
+Output - Advanced
+=================
+The effect of calling write() multiple times on a single file will vary
+depending on the file format, and is best avoided unless you have a strong
+reason to do so.
+
+Trying this for certain alignment formats (e.g. phylip, clustal, stockholm)
+would have the effect of concatenating several multiple sequence alignments
+together. Such files are created by the PHYLIP suite of programs for
+bootstrap analysis.
+
+For sequential files formats (e.g. fasta, genbank) each "record block" holds
+a single sequence. For these files it would probably be safe to call
+write() multiple times.
+
+File Formats
+============
+When specifying the file format, use lowercase strings. The same format
+names are also used in Bio.AlignIO and include the following:
+
+ - ace - Reads the contig sequences from an ACE assembly file.
+ - embl - The EMBL flat file format. Uses Bio.GenBank internally.
+ - fasta - The generic sequence file format where each record starts with
+ an identifer line starting with a ">" character, followed by
+ lines of sequence.
+ - fastq - A "FASTA like" format used by Sanger which also stores PHRED
+ sequence quality values.
+ - fastq-solexa - The Solexa/Illumnia variant of the Sanger FASTQ format which
+ encodes Solexa quality scores (not PHRED quality scores).
+ - genbank - The GenBank or GenPept flat file format.
+ - gb - An alias for "genbank", for consistency with NCBI Entrez Utilities
+ - ig - The IntelliGenetics file format, apparently the same as the
+ MASE alignment format.
+ - phd - Output from PHRED, used by PHRAP and CONSED for input.
+ - pir - A "FASTA like" format introduced by the National Biomedical
+ Research Foundation (NBRF) for the Protein Information Resource
+ (PIR) database, now part of UniProt.
+ - swiss - Plain text Swiss-Prot aka UniProt format.
+ - tab - Simple two column tab separated sequence files, where each
+ line holds a record's identifier and sequence. For example,
+ this is used as by Aligent's eArray software when saving
+ microarray probes in a minimal tab delimited text file.
+ - qual - A "FASTA like" format holding PHRED quality values from
+ sequencing DNA, but no actual sequences (usually provided
+ in separate FASTA files).
+
+Note that while Bio.SeqIO can read all the above file formats, it cannot
+write to all of them.
+
+You can also use any file format supported by Bio.AlignIO, such as "nexus",
+"phlip" and "stockholm", which gives you access to the individual sequences
+making up each alignment as SeqRecords.
+"""
+__docformat__ = "epytext en" #not just plaintext
+
+#TODO
+# - define policy on reading aligned sequences with gaps in
+# (e.g. - and . characters) including how the alphabet interacts
+#
+# - Can we build the to_alignment(...) functionality
+# into the generic Alignment class instead?
+#
+# - How best to handle unique/non unique record.id when writing.
+# For most file formats reading such files is fine; The stockholm
+# parser would fail.
+#
+# - MSF multiple alignment format, aka GCG, aka PileUp format (*.msf)
+# http://www.bioperl.org/wiki/MSF_multiple_alignment_format
+
+"""
+FAO BioPython Developers
+========================
+The way I envision this SeqIO system working as that for any sequence file
+format we have an iterator that returns SeqRecord objects.
+
+This also applies to interlaced fileformats (like clustal - although that
+is now handled via Bio.AlignIO instead) where the file cannot be read record
+by record. You should still return an iterator, even if the implementation
+could just as easily return a list.
+
+These file format specific sequence iterators may be implemented as:
+* Classes which take a handle for __init__ and provide the __iter__ method
+* Functions that take a handle, and return an iterator object
+* Generator functions that take a handle, and yield SeqRecord objects
+
+It is then trivial to turn this iterator into a list of SeqRecord objects,
+an in memory dictionary, or a multiple sequence alignment object.
+
+For building the dictionary by default the id propery of each SeqRecord is
+used as the key. You should always populate the id property, and it should
+be unique in most cases. For some file formats the accession number is a good
+choice. If the file itself contains ambiguous identifiers, don't try and
+dis-ambiguate them - return them as is.
+
+When adding a new file format, please use the same lower case format name
+as BioPerl, or if they have not defined one, try the names used by EMBOSS.
+
+See also http://biopython.org/wiki/SeqIO_dev
+
+--Peter
+"""
+
+import os
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.Align.Generic import Alignment
+from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
+
+import AceIO
+import FastaIO
+import IgIO #IntelliGenetics or MASE format
+import InsdcIO #EMBL and GenBank
+import PhdIO
+import PirIO
+import SwissIO
+import TabIO
+import QualityIO #FastQ and qual files
+
+
+#Convention for format names is "mainname-subtype" in lower case.
+#Please use the same names as BioPerl where possible.
+#
+#Note that this simple system copes with defining
+#multiple possible iterators for a given format/extension
+#with the -subtype suffix
+#
+#Most alignment file formats will be handled via Bio.AlignIO
+
+_FormatToIterator ={"fasta" : FastaIO.FastaIterator,
+ "gb" : InsdcIO.GenBankIterator,
+ "genbank" : InsdcIO.GenBankIterator,
+ "genbank-cds" : InsdcIO.GenBankCdsFeatureIterator,
+ "embl" : InsdcIO.EmblIterator,
+ "embl-cds" : InsdcIO.EmblCdsFeatureIterator,
+ "ig" : IgIO.IgIterator,
+ "swiss" : SwissIO.SwissIterator,
+ "phd" : PhdIO.PhdIterator,
+ "ace" : AceIO.AceIterator,
+ "tab" : TabIO.TabIterator,
+ "pir" : PirIO.PirIterator,
+ "fastq" : QualityIO.FastqPhredIterator,
+ "fastq-solexa" : QualityIO.FastqSolexaIterator,
+ "qual" : QualityIO.QualPhredIterator,
+ }
+
+_FormatToWriter ={"fasta" : FastaIO.FastaWriter,
+ "gb" : InsdcIO.GenBankWriter,
+ "genbank" : InsdcIO.GenBankWriter,
+ "tab" : TabIO.TabWriter,
+ "fastq" : QualityIO.FastqPhredWriter,
+ "fastq-solexa" : QualityIO.FastqSolexaWriter,
+ "qual" : QualityIO.QualPhredWriter,
+ }
+
+def write(sequences, handle, format) :
+ """Write complete set of sequences to a file.
+
+ - sequences - A list (or iterator) of SeqRecord objects.
+ - handle - File handle object to write to.
+ - format - lower case string describing the file format to write.
+
+ You should close the handle after calling this function.
+
+ Returns the number of records written (as an integer).
+ """
+ from Bio import AlignIO
+
+ #Try and give helpful error messages:
+ if isinstance(handle, basestring) :
+ raise TypeError("Need a file handle, not a string (i.e. not a filename)")
+ if not isinstance(format, basestring) :
+ raise TypeError("Need a string for the file format (lower case)")
+ if not format :
+ raise ValueError("Format required (lower case string)")
+ if format != format.lower() :
+ raise ValueError("Format string '%s' should be lower case" % format)
+ if isinstance(sequences,SeqRecord):
+ raise ValueError("Use a SeqRecord list/iterator, not just a single SeqRecord")
+
+ #Map the file format to a writer class
+ if format in _FormatToWriter :
+ writer_class = _FormatToWriter[format]
+ count = writer_class(handle).write_file(sequences)
+ elif format in AlignIO._FormatToWriter :
+ #Try and turn all the records into a single alignment,
+ #and write that using Bio.AlignIO
+ alignment = to_alignment(sequences)
+ alignment_count = AlignIO.write([alignment], handle, format)
+ assert alignment_count == 1, "Internal error - the underlying writer " \
+ + " should have returned 1, not %s" % repr(alignment_count)
+ count = len(alignment.get_all_seqs())
+ del alignment_count, alignment
+ elif format in _FormatToIterator or format in AlignIO._FormatToIterator :
+ raise ValueError("Reading format '%s' is supported, but not writing" \
+ % format)
+ else :
+ raise ValueError("Unknown format '%s'" % format)
+
+ assert isinstance(count, int), "Internal error - the underlying writer " \
+ + " should have returned the record count, not %s" % repr(count)
+ return count
+
+def parse(handle, format, alphabet=None) :
+ r"""Turns a sequence file into an iterator returning SeqRecords.
+
+ - handle - handle to the file.
+ - format - lower case string describing the file format.
+ - alphabet - optional Alphabet object, useful when the sequence type
+ cannot be automatically inferred from the file itself
+ (e.g. format="fasta" or "tab")
+
+ Typical usage, opening a file to read in, and looping over the record(s):
+
+ >>> from Bio import SeqIO
+ >>> filename = "Nucleic/sweetpea.nu"
+ >>> for record in SeqIO.parse(open(filename,"rU"), "fasta") :
+ ... print "ID", record.id
+ ... print "Sequence length", len(record)
+ ... print "Sequence alphabet", record.seq.alphabet
+ ID gi|3176602|gb|U78617.1|LOU78617
+ Sequence length 309
+ Sequence alphabet SingleLetterAlphabet()
+
+ For file formats like FASTA where the alphabet cannot be determined, it
+ may be useful to specify the alphabet explicitly:
+
+ >>> from Bio import SeqIO
+ >>> from Bio.Alphabet import generic_dna
+ >>> filename = "Nucleic/sweetpea.nu"
+ >>> for record in SeqIO.parse(open(filename,"rU"), "fasta", generic_dna) :
+ ... print "ID", record.id
+ ... print "Sequence length", len(record)
+ ... print "Sequence alphabet", record.seq.alphabet
+ ID gi|3176602|gb|U78617.1|LOU78617
+ Sequence length 309
+ Sequence alphabet DNAAlphabet()
+
+ If you have a string 'data' containing the file contents, you must
+ first turn this into a handle in order to parse it:
+
+ >>> data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n"
+ >>> from Bio import SeqIO
+ >>> from StringIO import StringIO
+ >>> for record in SeqIO.parse(StringIO(data), "fasta") :
+ ... print record.id, record.seq
+ Alpha ACCGGATGTA
+ Beta AGGCTCGGTTA
+
+ Use the Bio.SeqIO.read(handle, format) function when you expect a single
+ record only.
+ """
+ #NOTE - The above docstring has some raw \n characters needed
+ #for the StringIO example, hense the whole docstring is in raw
+ #string more (see the leading r before the opening quote).
+ from Bio import AlignIO
+
+ #Try and give helpful error messages:
+ if isinstance(handle, basestring) :
+ raise TypeError("Need a file handle, not a string (i.e. not a filename)")
+ if not isinstance(format, basestring) :
+ raise TypeError("Need a string for the file format (lower case)")
+ if not format :
+ raise ValueError("Format required (lower case string)")
+ if format != format.lower() :
+ raise ValueError("Format string '%s' should be lower case" % format)
+ if alphabet is not None and not (isinstance(alphabet, Alphabet) or \
+ isinstance(alphabet, AlphabetEncoder)) :
+ raise ValueError("Invalid alphabet, %s" % repr(alphabet))
+
+ #Map the file format to a sequence iterator:
+ if format in _FormatToIterator :
+ iterator_generator = _FormatToIterator[format]
+ if alphabet is None :
+ return iterator_generator(handle)
+ try :
+ return iterator_generator(handle, alphabet=alphabet)
+ except :
+ return _force_alphabet(iterator_generator(handle), alphabet)
+ elif format in AlignIO._FormatToIterator :
+ #Use Bio.AlignIO to read in the alignments
+ #TODO - Once we drop support for Python 2.3, this helper function can be
+ #replaced with a generator expression.
+ return _iterate_via_AlignIO(handle, format, alphabet)
+ else :
+ raise ValueError("Unknown format '%s'" % format)
+
+#This is a generator function
+def _iterate_via_AlignIO(handle, format, alphabet) :
+ """Iterate over all records in several alignments (PRIVATE)."""
+ from Bio import AlignIO
+ for align in AlignIO.parse(handle, format, alphabet=alphabet) :
+ for record in align :
+ yield record
+
+def _force_alphabet(record_iterator, alphabet) :
+ """Iterate over records, over-riding the alphabet (PRIVATE)."""
+ #Assume the alphabet argument has been pre-validated
+ given_base_class = _get_base_alphabet(alphabet).__class__
+ for record in record_iterator :
+ if isinstance(_get_base_alphabet(record.seq.alphabet),
+ given_base_class) :
+ record.seq.alphabet = alphabet
+ yield record
+ else :
+ raise ValueError("Specified alphabet %s clashes with "\
+ "that determined from the file, %s" \
+ % (repr(alphabet), repr(record.seq.alphabet)))
+
+def read(handle, format, alphabet=None) :
+ """Turns a sequence file into a single SeqRecord.
+
+ - handle - handle to the file.
+ - format - string describing the file format.
+ - alphabet - optional Alphabet object, useful when the sequence type
+ cannot be automatically inferred from the file itself
+ (e.g. format="fasta" or "tab")
+
+ This function is for use parsing sequence files containing
+ exactly one record. For example, reading a GenBank file:
+
+ >>> from Bio import SeqIO
+ >>> record = SeqIO.read(open("GenBank/arab1.gb", "rU"), "genbank")
+ >>> print "ID", record.id
+ ID AC007323.5
+ >>> print "Sequence length", len(record)
+ Sequence length 86436
+ >>> print "Sequence alphabet", record.seq.alphabet
+ Sequence alphabet IUPACAmbiguousDNA()
+
+ If the handle contains no records, or more than one record,
+ an exception is raised. For example:
+
+ >>> from Bio import SeqIO
+ >>> record = SeqIO.read(open("GenBank/cor6_6.gb", "rU"), "genbank")
+ Traceback (most recent call last):
+ ...
+ ValueError: More than one record found in handle
+
+ If however you want the first record from a file containing
+ multiple records this function would raise an exception (as
+ shown in the example above). Instead use:
+
+ >>> from Bio import SeqIO
+ >>> record = SeqIO.parse(open("GenBank/cor6_6.gb", "rU"), "genbank").next()
+ >>> print "First record's ID", record.id
+ First record's ID X55053.1
+
+ Use the Bio.SeqIO.parse(handle, format) function if you want
+ to read multiple records from the handle.
+ """
+ iterator = parse(handle, format, alphabet)
+ try :
+ first = iterator.next()
+ except StopIteration :
+ first = None
+ if first is None :
+ raise ValueError("No records found in handle")
+ try :
+ second = iterator.next()
+ except StopIteration :
+ second = None
+ if second is not None :
+ raise ValueError("More than one record found in handle")
+ return first
+
+def to_dict(sequences, key_function=None) :
+ """Turns a sequence iterator or list into a dictionary.
+
+ - sequences - An iterator that returns SeqRecord objects,
+ or simply a list of SeqRecord objects.
+ - key_function - Optional function which when given a SeqRecord
+ returns a unique string for the dictionary key.
+
+ e.g. key_function = lambda rec : rec.name
+ or, key_function = lambda rec : rec.description.split()[0]
+
+ If key_function is ommitted then record.id is used, on the
+ assumption that the records objects returned are SeqRecords
+ with a unique id field.
+
+ If there are duplicate keys, an error is raised.
+
+ Example usage, defaulting to using the record.id as key:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("GenBank/cor6_6.gb", "rU")
+ >>> format = "genbank"
+ >>> id_dict = SeqIO.to_dict(SeqIO.parse(handle, format))
+ >>> print id_dict.keys()
+ ['L31939.1', 'AJ237582.1', 'X62281.1', 'AF297471.1', 'X55053.1', 'M81224.1']
+ >>> print id_dict["L31939.1"].description
+ Brassica rapa (clone bif72) kin mRNA, complete cds.
+
+ A more complex example, using the key_function argument in order to use
+ a sequence checksum as the dictionary key:
+
+ >>> from Bio import SeqIO
+ >>> from Bio.SeqUtils.CheckSum import seguid
+ >>> handle = open("GenBank/cor6_6.gb", "rU")
+ >>> format = "genbank"
+ >>> seguid_dict = SeqIO.to_dict(SeqIO.parse(handle, format),
+ ... key_function = lambda rec : seguid(rec.seq))
+ >>> for key, record in seguid_dict.iteritems() :
+ ... print key, record.id
+ SabZaA4V2eLE9/2Fm5FnyYy07J4 X55053.1
+ l7gjJFE6W/S1jJn5+1ASrUKW/FA X62281.1
+ /wQvmrl87QWcm9llO4/efg23Vgg AJ237582.1
+ TtWsXo45S3ZclIBy4X/WJc39+CY M81224.1
+ uVEYeAQSV5EDQOnFoeMmVea+Oow AF297471.1
+ BUg6YxXSKWEcFFH0L08JzaLGhQs L31939.1
+ """
+ if key_function is None :
+ key_function = lambda rec : rec.id
+
+ d = dict()
+ for record in sequences :
+ key = key_function(record)
+ if key in d :
+ raise ValueError("Duplicate key '%s'" % key)
+ d[key] = record
+ return d
+
+
+def to_alignment(sequences, alphabet=None, strict=True) :
+ """Returns a multiple sequence alignment (OBSOLETE).
+
+ - sequences -An iterator that returns SeqRecord objects,
+ or simply a list of SeqRecord objects. All
+ the record sequences must be the same length.
+ - alphabet - Optional alphabet. Stongly recommended.
+ - strict - Optional, defaults to True. Should error checking
+ be done?
+
+ Using this function is now discouraged. Rather doing this:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Clustalw/protein.aln")
+ >>> alignment = SeqIO.to_alignment(SeqIO.parse(handle, "clustal"))
+ >>> handle.close()
+
+ You are now encouraged to use Bio.AlignIO instead, e.g.
+
+ >>> from Bio import AlignIO
+ >>> handle = open("Clustalw/protein.aln")
+ >>> alignment = AlignIO.read(handle, "clustal")
+ >>> handle.close()
+ """
+ #TODO - Move this functionality into the Alignment class instead?
+ from Bio.Alphabet import generic_alphabet
+ from Bio.Alphabet import _consensus_alphabet
+ if alphabet is None :
+ sequences = list(sequences)
+ alphabet = _consensus_alphabet([rec.seq.alphabet for rec in sequences \
+ if rec.seq is not None])
+
+ if not (isinstance(alphabet, Alphabet) or isinstance(alphabet, AlphabetEncoder)) :
+ raise ValueError("Invalid alphabet")
+
+ alignment_length = None
+ alignment = Alignment(alphabet)
+ for record in sequences :
+ if strict :
+ if alignment_length is None :
+ alignment_length = len(record.seq)
+ elif alignment_length != len(record.seq) :
+ raise ValueError("Sequences must all be the same length")
+
+ assert isinstance(record.seq.alphabet, Alphabet) \
+ or isinstance(record.seq.alphabet, AlphabetEncoder), \
+ "Sequence does not have a valid alphabet"
+
+ #TODO - Move this alphabet comparison code into the Alphabet module/class?
+ #TODO - Is a normal alphabet "ungapped" by default, or does it just mean
+ #undecided?
+ if isinstance(record.seq.alphabet, Alphabet) \
+ and isinstance(alphabet, Alphabet) :
+ #Comparing two non-gapped alphabets
+ if not isinstance(record.seq.alphabet, alphabet.__class__) :
+ raise ValueError("Incompatible sequence alphabet " \
+ + "%s for %s alignment" \
+ % (record.seq.alphabet, alphabet))
+ elif isinstance(record.seq.alphabet, AlphabetEncoder) \
+ and isinstance(alphabet, Alphabet) :
+ raise ValueError("Sequence has a gapped alphabet, alignment does not")
+ elif isinstance(record.seq.alphabet, Alphabet) \
+ and isinstance(alphabet, Gapped) :
+ #Sequence isn't gapped, alignment is.
+ if not isinstance(record.seq.alphabet, alphabet.alphabet.__class__) :
+ raise ValueError("Incompatible sequence alphabet " \
+ + "%s for %s alignment" \
+ % (record.seq.alphabet, alphabet))
+ else :
+ #Comparing two gapped alphabets
+ if not isinstance(record.seq.alphabet, alphabet.__class__) :
+ raise ValueError("Incompatible sequence alphabet " \
+ + "%s for %s alignment" \
+ % (record.seq.alphabet, alphabet))
+ if record.seq.alphabet.gap_char != alphabet.gap_char :
+ raise ValueError("Sequence gap characters != alignment gap char")
+ #ToDo, additional checks on the specified alignment...
+ #Should we look at the alphabet.contains() method?
+ if record.seq is None :
+ raise TypeError("SeqRecord (id=%s) has None for its sequence." % record.id)
+
+ #This is abusing the "private" records list,
+ #we should really have a method like add_sequence
+ #but which takes SeqRecord objects. See also Bug 1944
+ alignment._records.append(record)
+ return alignment
+
+def _test():
+ """Run the Bio.SeqIO module's doctests.
+
+ This will try and locate the unit tests directory, and run the doctests
+ from there in order that the relative paths used in the examples work.
+ """
+ import doctest
+ import os
+ if os.path.isdir(os.path.join("..","..","Tests")) :
+ print "Runing doctests..."
+ cur_dir = os.path.abspath(os.curdir)
+ os.chdir(os.path.join("..","..","Tests"))
+ doctest.testmod()
+ os.chdir(cur_dir)
+ del cur_dir
+ print "Done"
+
+if __name__ == "__main__":
+ #Run the doctests
+ _test()
--- /dev/null
+# Copyright 2000-2002 Andrew Dalke.
+# Copyright 2002-2004 Brad Chapman.
+# Copyright 2006-2009 by Peter Cock.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+"""Represent a Sequence Record, a sequence with annotation."""
+__docformat__ = "epytext en" #Simple markup to show doctests nicely
+
+# NEEDS TO BE SYNCH WITH THE REST OF BIOPYTHON AND BIOPERL
+# In particular, the SeqRecord and BioSQL.BioSeq.DBSeqRecord classes
+# need to be in sync (this is the BioSQL "Database SeqRecord", see
+# also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
+
+class _RestrictedDict(dict):
+ """Dict which only allows sequences of given length as values (PRIVATE).
+
+ This simple subclass of the python dictionary is used in the SeqRecord
+ object for holding per-letter-annotations. This class is intended to
+ prevent simple errors by only allowing python sequences (e.g. lists,
+ strings and tuples) to be stored, and only if their length matches that
+ expected (the length of the SeqRecord's seq object). It cannot however
+ prevent the entries being edited in situ (for example appending entries
+ to a list).
+ """
+ def __init__(self, length) :
+ """Create an EMPTY restricted dictionary."""
+ dict.__init__(self)
+ self._length = int(length)
+ def __setitem__(self, key, value) :
+ if not hasattr(value,"__len__") or not hasattr(value,"__getitem__") \
+ or len(value) != self._length :
+ raise TypeError("We only allow python sequences (lists, tuples or "
+ "strings) of length %i." % self._length)
+ dict.__setitem__(self, key, value)
+
+class SeqRecord(object):
+ """A SeqRecord object holds a sequence and information about it.
+
+ Main attributes:
+ - id - Identifier such as a locus tag (string)
+ - seq - The sequence itself (Seq object)
+
+ Additional attributes:
+ - name - Sequence name, e.g. gene name (string)
+ - description - Additional text (string)
+ - dbxrefs - List of database cross references (list of strings)
+ - features - Any (sub)features defined (list of SeqFeature objects)
+ - annotations - Further information about the whole sequence (dictionary)
+ Most entries are lists of strings.
+ - letter_annotations - Per letter/symbol annotation (restricted
+ dictionary). This holds python sequences (lists, strings
+ or tuples) whose length matches that of the sequence.
+ A typical use would be to hold a list of integers
+ representing sequencing quality scores, or a string
+ representing the secondary structure.
+
+ You will typically use Bio.SeqIO to read in sequences from files as
+ SeqRecord objects. However, you may want to create your own SeqRecord
+ objects directly (see the __init__ method for further details):
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.SeqRecord import SeqRecord
+ >>> from Bio.Alphabet import IUPAC
+ >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
+ ... IUPAC.protein),
+ ... id="YP_025292.1", name="HokC",
+ ... description="toxic membrane protein")
+ >>> print record
+ ID: YP_025292.1
+ Name: HokC
+ Description: toxic membrane protein
+ Number of features: 0
+ Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
+
+ If you want to save SeqRecord objects to a sequence file, use Bio.SeqIO
+ for this. For the special case where you want the SeqRecord turned into
+ a string in a particular file format there is a format method which uses
+ Bio.SeqIO internally:
+
+ >>> print record.format("fasta")
+ >YP_025292.1 toxic membrane protein
+ MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
+ <BLANKLINE>
+ """
+ def __init__(self, seq, id = "<unknown id>", name = "<unknown name>",
+ description = "<unknown description>", dbxrefs = None,
+ features = None):
+ """Create a SeqRecord.
+
+ Arguments:
+ - seq - Sequence, required (Seq or Mutable object)
+ - id - Sequence identifier, recommended (string)
+ - name - Sequence name, optional (string)
+ - description - Sequence description, optional (string)
+ - dbxrefs - Database cross references, optional (list of strings)
+ - features - Any (sub)features, optional (list of SeqFeature objects)
+
+ You will typically use Bio.SeqIO to read in sequences from files as
+ SeqRecord objects. However, you may want to create your own SeqRecord
+ objects directly.
+
+ Note that while an id is optional, we strongly recommend you supply a
+ unique id string for each record. This is especially important
+ if you wish to write your sequences to a file.
+
+ If you don't have the actual sequence, but you do know its length,
+ then using the UnknownSeq object from Bio.Seq is appropriate.
+
+ You can create a 'blank' SeqRecord object, and then populate the
+ attributes later. Note that currently the annotations and the
+ letter_annotations dictionaries cannot be specified when creating
+ the SeqRecord.
+ """
+ if id is not None and not isinstance(id, basestring) :
+ #Lots of existing code uses id=None... this may be a bad idea.
+ raise TypeError("id argument should be a string")
+ if not isinstance(name, basestring) :
+ raise TypeError("name argument should be a string")
+ if not isinstance(description, basestring) :
+ raise TypeError("description argument should be a string")
+ if dbxrefs is not None and not isinstance(dbxrefs, list) :
+ raise TypeError("dbxrefs argument should be a list (of strings)")
+ if features is not None and not isinstance(features, list) :
+ raise TypeError("features argument should be a list (of SeqFeature objects)")
+ self._seq = seq
+ self.id = id
+ self.name = name
+ self.description = description
+ if dbxrefs is None:
+ dbxrefs = []
+ self.dbxrefs = dbxrefs
+ # annotations about the whole sequence
+ self.annotations = {}
+
+ # annotations about each letter in the sequence
+ if seq is None :
+ #Should we allow this and use a normal unrestricted dict?
+ self._per_letter_annotations = _RestrictedDict(length=0)
+ else :
+ try :
+ self._per_letter_annotations = _RestrictedDict(length=len(seq))
+ except :
+ raise TypeError("seq argument should be a Seq or MutableSeq")
+
+ # annotations about parts of the sequence
+ if features is None:
+ features = []
+ self.features = features
+
+ #TODO - Just make this a read only property?
+ def _set_per_letter_annotations(self, value) :
+ if not isinstance(value, dict) :
+ raise TypeError("The per-letter-annotations should be a "
+ "(restricted) dictionary.")
+ #Turn this into a restricted-dictionary (and check the entries)
+ try :
+ self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
+ except AttributeError :
+ #e.g. seq is None
+ self._per_letter_annotations = _RestrictedDict(length=0)
+ self._per_letter_annotations.update(value)
+ letter_annotations = property( \
+ fget=lambda self : self._per_letter_annotations,
+ fset=_set_per_letter_annotations,
+ doc="""Dictionary of per-letter-annotation for the sequence.
+
+ For example, this can hold quality scores used in FASTQ or QUAL files.
+ Consider this example using Bio.SeqIO to read in an example Solexa
+ variant FASTQ file as a SeqRecord:
+
+ >>> from Bio import SeqIO
+ >>> handle = open("Quality/solexa.fastq", "rU")
+ >>> record = SeqIO.read(handle, "fastq-solexa")
+ >>> handle.close()
+ >>> print record.id, record.seq
+ slxa_0013_1_0001_24 ACAAAAATCACAAGCATTCTTATACACC
+ >>> print record.letter_annotations.keys()
+ ['solexa_quality']
+ >>> print record.letter_annotations["solexa_quality"]
+ [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -6, -1, -1, -4, -1, -4, -19, -10, -27, -18]
+
+ The per-letter-annotaions get sliced automatically if you slice the
+ parent SeqRecord, for example taking the last ten bases:
+
+ >>> sub_record = record[-10:]
+ >>> print sub_record.id, sub_record.seq
+ slxa_0013_1_0001_24 CTTATACACC
+ >>> print sub_record.letter_annotations["solexa_quality"]
+ [-6, -1, -1, -4, -1, -4, -19, -10, -27, -18]
+
+ Any python sequence (i.e. list, tuple or string) can be recorded in
+ the SeqRecord's letter_annotations dictionary as long as the length
+ matches that of the SeqRecord's sequence. e.g.
+
+ >>> len(sub_record.letter_annotations)
+ 1
+ >>> sub_record.letter_annotations["dummy"] = "abcdefghij"
+ >>> len(sub_record.letter_annotations)
+ 2
+
+ You can delete entries from the letter_annotations dictionary as usual:
+
+ >>> del sub_record.letter_annotations["solexa_quality"]
+ >>> sub_record.letter_annotations
+ {'dummy': 'abcdefghij'}
+
+ You can completely clear the dictionary easily as follows:
+
+ >>> sub_record.letter_annotations = {}
+ >>> sub_record.letter_annotations
+ {}
+ """)
+
+ def _set_seq(self, value) :
+ #TODO - Add a deprecation warning that the seq should be write only?
+ if self._per_letter_annotations :
+ #TODO - Make this a warning? Silently empty the dictionary?
+ raise ValueError("You must empty the letter annotations first!")
+ self._seq = value
+ try :
+ self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
+ except AttributeError :
+ #e.g. seq is None
+ self._per_letter_annotations = _RestrictedDict(length=0)
+
+ seq = property(fget=lambda self : self._seq,
+ fset=_set_seq,
+ doc="The sequence itself, as a Seq or MutableSeq object.")
+
+ def __getitem__(self, index) :
+ """Returns a sub-sequence or an individual letter.
+
+ Splicing, e.g. my_record[5:10], returns a new SeqRecord for
+ that sub-sequence with approriate annotation preserved. The
+ name, id and description are kept.
+
+ Any per-letter-annotations are sliced to match the requested
+ sub-sequence. Unless a stride is used, all those features
+ which fall fully within the subsequence are included (with
+ their locations adjusted accordingly).
+
+ However, the annotations dictionary and the dbxrefs list are
+ not used for the new SeqRecord, as in general they may not
+ apply to the subsequence. If you want to preserve them, you
+ must explictly copy them to the new SeqRecord yourself.
+
+ Using an integer index, e.g. my_record[5] is shorthand for
+ extracting that letter from the sequence, my_record.seq[5].
+
+ For example, consider this short protein and its secondary
+ structure as encoded by the PDB (e.g. H for alpha helices),
+ plus a simple feature for its histidine self phosphorylation
+ site:
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.SeqRecord import SeqRecord
+ >>> from Bio.SeqFeature import SeqFeature, FeatureLocation
+ >>> from Bio.Alphabet import IUPAC
+ >>> rec = SeqRecord(Seq("MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLAT"
+ ... "EMMSEQDGYLAESINKDIEECNAIIEQFIDYLR",
+ ... IUPAC.protein),
+ ... id="1JOY", name="EnvZ",
+ ... description="Homodimeric domain of EnvZ from E. coli")
+ >>> rec.letter_annotations["secondary_structure"] = \
+ " S SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT "
+ >>> rec.features.append(SeqFeature(FeatureLocation(20,21),
+ ... type = "Site"))
+
+ Now let's have a quick look at the full record,
+
+ >>> print rec
+ ID: 1JOY
+ Name: EnvZ
+ Description: Homodimeric domain of EnvZ from E. coli
+ Number of features: 1
+ Per letter annotation for: secondary_structure
+ Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR', IUPACProtein())
+ >>> print rec.letter_annotations["secondary_structure"]
+ S SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT
+ >>> print rec.features[0].location
+ [20:21]
+
+ Now let's take a sub sequence, here chosen as the first (fractured)
+ alpha helix which includes the histidine phosphorylation site:
+
+ >>> sub = rec[11:41]
+ >>> print sub
+ ID: 1JOY
+ Name: EnvZ
+ Description: Homodimeric domain of EnvZ from E. coli
+ Number of features: 1
+ Per letter annotation for: secondary_structure
+ Seq('RTLLMAGVSHDLRTPLTRIRLATEMMSEQD', IUPACProtein())
+ >>> print sub.letter_annotations["secondary_structure"]
+ HHHHHTTTHHHHHHHHHHHHHHHHHHHHHH
+ >>> print sub.features[0].location
+ [9:10]
+
+ You can also of course omit the start or end values, for
+ example to get the first ten letters only:
+
+ >>> print rec[:10]
+ ID: 1JOY
+ Name: EnvZ
+ Description: Homodimeric domain of EnvZ from E. coli
+ Number of features: 0
+ Per letter annotation for: secondary_structure
+ Seq('MAAGVKQLAD', IUPACProtein())
+
+ Or for the last ten letters:
+
+ >>> print rec[-10:]
+ ID: 1JOY
+ Name: EnvZ
+ Description: Homodimeric domain of EnvZ from E. coli
+ Number of features: 0
+ Per letter annotation for: secondary_structure
+ Seq('IIEQFIDYLR', IUPACProtein())
+
+ If you omit both, then you get a copy of the original record (although
+ lacking the annotations and dbxrefs):
+
+ >>> print rec[:]
+ ID: 1JOY
+ Name: EnvZ
+ Description: Homodimeric domain of EnvZ from E. coli
+ Number of features: 1
+ Per letter annotation for: secondary_structure
+ Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR', IUPACProtein())
+
+ Finally, indexing with a simple integer is shorthand for pulling out
+ that letter from the sequence directly:
+
+ >>> rec[5]
+ 'K'
+ >>> rec.seq[5]
+ 'K'
+ """
+ if isinstance(index, int) :
+ #NOTE - The sequence level annotation like the id, name, etc
+ #do not really apply to a single character. However, should
+ #we try and expose any per-letter-annotation here? If so how?
+ return self.seq[index]
+ elif isinstance(index, slice) :
+ if self.seq is None :
+ raise ValueError("If the sequence is None, we cannot slice it.")
+ parent_length = len(self)
+ answer = self.__class__(self.seq[index],
+ id=self.id,
+ name=self.name,
+ description=self.description)
+ #TODO - The desription may no longer apply.
+ #It would be safer to change it to something
+ #generic like "edited" or the default value.
+
+ #Don't copy the annotation dict and dbxefs list,
+ #they may not apply to a subsequence.
+ #answer.annotations = dict(self.annotations.iteritems())
+ #answer.dbxrefs = self.dbxrefs[:]
+
+ #TODO - Cope with strides by generating ambiguous locations?
+ if index.step is None or index.step == 1 :
+ #Select relevant features, add them with shifted locations
+ if index.start is None :
+ start = 0
+ else :
+ start = index.start
+ if index.stop is None :
+ stop = -1
+ else :
+ stop = index.stop
+ if (start < 0 or stop < 0) and parent_length == 0 :
+ raise ValueError, \
+ "Cannot support negative indices without the sequence length"
+ if start < 0 :
+ start = parent_length - start
+ if stop < 0 :
+ stop = parent_length - stop + 1
+ #assert str(self.seq)[index] == str(self.seq)[start:stop]
+ for f in self.features :
+ if start <= f.location.start.position \
+ and f.location.end.position < stop :
+ answer.features.append(f._shift(-start))
+
+ #Slice all the values to match the sliced sequence
+ #(this should also work with strides, even negative strides):
+ for key, value in self.letter_annotations.iteritems() :
+ answer._per_letter_annotations[key] = value[index]
+
+ return answer
+ raise ValueError, "Invalid index"
+
+ def __iter__(self) :
+ """Iterate over the letters in the sequence.
+
+ For example, using Bio.SeqIO to read in a protein FASTA file:
+
+ >>> from Bio import SeqIO
+ >>> record = SeqIO.read(open("Amino/loveliesbleeding.pro"),"fasta")
+ >>> for amino in record :
+ ... print amino
+ ... if amino == "L" : break
+ X
+ A
+ G
+ L
+ >>> print record.seq[3]
+ L
+
+ This is just a shortcut for iterating over the sequence directly:
+
+ >>> for amino in record.seq :
+ ... print amino
+ ... if amino == "L" : break
+ X
+ A
+ G
+ L
+ >>> print record.seq[3]
+ L
+
+ Note that this does not facilitate iteration together with any
+ per-letter-annotation. However, you can achieve that using the
+ python zip function on the record (or its sequence) and the relevant
+ per-letter-annotation:
+
+ >>> from Bio import SeqIO
+ >>> rec = SeqIO.read(open("Quality/solexa.fastq", "rU"),
+ ... "fastq-solexa")
+ >>> print rec.id, rec.seq
+ slxa_0013_1_0001_24 ACAAAAATCACAAGCATTCTTATACACC
+ >>> print rec.letter_annotations.keys()
+ ['solexa_quality']
+ >>> for nuc, qual in zip(rec,rec.letter_annotations["solexa_quality"]) :
+ ... if qual < -10 :
+ ... print nuc, qual
+ C -19
+ C -27
+ C -18
+
+ You may agree that using zip(rec.seq, ...) is more explicit than using
+ zip(rec, ...) as shown above.
+ """
+ return iter(self.seq)
+
+ def __str__(self) :
+ """A human readable summary of the record and its annotation (string).
+
+ The python built in function str works by calling the object's ___str__
+ method. e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.SeqRecord import SeqRecord
+ >>> from Bio.Alphabet import IUPAC
+ >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
+ ... IUPAC.protein),
+ ... id="YP_025292.1", name="HokC",
+ ... description="toxic membrane protein, small")
+ >>> print str(record)
+ ID: YP_025292.1
+ Name: HokC
+ Description: toxic membrane protein, small
+ Number of features: 0
+ Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
+
+ In this example you don't actually need to call str explicity, as the
+ print command does this automatically:
+
+ >>> print record
+ ID: YP_025292.1
+ Name: HokC
+ Description: toxic membrane protein, small
+ Number of features: 0
+ Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
+
+ Note that long sequences are shown truncated.
+ """
+ lines = []
+ if self.id : lines.append("ID: %s" % self.id)
+ if self.name : lines.append("Name: %s" % self.name)
+ if self.description : lines.append("Description: %s" % self.description)
+ if self.dbxrefs : lines.append("Database cross-references: " \
+ + ", ".join(self.dbxrefs))
+ lines.append("Number of features: %i" % len(self.features))
+ for a in self.annotations:
+ lines.append("/%s=%s" % (a, str(self.annotations[a])))
+ if self.letter_annotations :
+ lines.append("Per letter annotation for: " \
+ + ", ".join(self.letter_annotations.keys()))
+ #Don't want to include the entire sequence,
+ #and showing the alphabet is useful:
+ lines.append(repr(self.seq))
+ return "\n".join(lines)
+
+ def __repr__(self) :
+ """A concise summary of the record for debugging (string).
+
+ The python built in function repr works by calling the object's ___repr__
+ method. e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.SeqRecord import SeqRecord
+ >>> from Bio.Alphabet import generic_protein
+ >>> rec = SeqRecord(Seq("MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT"
+ ... +"GEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQ"
+ ... +"SGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQ"
+ ... +"PQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF",
+ ... generic_protein),
+ ... id="NP_418483.1", name="b4059",
+ ... description="ssDNA-binding protein",
+ ... dbxrefs=["ASAP:13298", "GI:16131885", "GeneID:948570"])
+ >>> print repr(rec)
+ SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF', ProteinAlphabet()), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])
+
+ At the python prompt you can also use this shorthand:
+
+ >>> rec
+ SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF', ProteinAlphabet()), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])
+
+ Note that long sequences are shown truncated.
+ """
+ return self.__class__.__name__ \
+ + "(seq=%s, id=%s, name=%s, description=%s, dbxrefs=%s)" \
+ % tuple(map(repr, (self.seq, self.id, self.name,
+ self.description, self.dbxrefs)))
+
+ def format(self, format) :
+ r"""Returns the record as a string in the specified file format.
+
+ The format should be a lower case string supported as an output
+ format by Bio.SeqIO, which is used to turn the SeqRecord into a
+ string. e.g.
+
+ >>> from Bio.Seq import Seq
+ >>> from Bio.SeqRecord import SeqRecord
+ >>> from Bio.Alphabet import IUPAC
+ >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
+ ... IUPAC.protein),
+ ... id="YP_025292.1", name="HokC",
+ ... description="toxic membrane protein")
+ >>> record.format("fasta")
+ '>YP_025292.1 toxic membrane protein\nMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\n'
+ >>> print record.format("fasta")
+ >YP_025292.1 toxic membrane protein
+ MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
+ <BLANKLINE>
+
+ The python print command automatically appends a new line, meaning
+ in this example a blank line is shown. If you look at the string
+ representation you can see there is a trailing new line (shown as
+ slash n) which is important when writing to a file or if
+ concatenating mutliple sequence strings together.
+
+ Note that this method will NOT work on every possible file format
+ supported by Bio.SeqIO (e.g. some are for multiple sequences only).
+ """
+ #See also the __format__ added for Python 2.6 / 3.0, PEP 3101
+ #See also the Bio.Align.Generic.Alignment class and its format()
+ return self.__format__(format)
+
+ def __format__(self, format_spec) :
+ """Returns the record as a string in the specified file format.
+
+ This method supports the python format() function added in
+ Python 2.6/3.0. The format_spec should be a lower case
+ string supported by Bio.SeqIO as an output file format.
+ See also the SeqRecord's format() method.
+ """
+ if format_spec:
+ from StringIO import StringIO
+ from Bio import SeqIO
+ handle = StringIO()
+ SeqIO.write([self], handle, format_spec)
+ return handle.getvalue()
+ else :
+ #Follow python convention and default to using __str__
+ return str(self)
+
+ def __len__(self) :
+ """Returns the length of the sequence.
+
+ For example, using Bio.SeqIO to read in a FASTA nucleotide file:
+
+ >>> from Bio import SeqIO
+ >>> record = SeqIO.read(open("Nucleic/sweetpea.nu"),"fasta")
+ >>> len(record)
+ 309
+ >>> len(record.seq)
+ 309
+ """
+ return len(self.seq)
+
+ def __nonzero__(self) :
+ """Returns True regardless of the length of the sequence.
+
+ This behaviour is for backwards compatibility, since until the
+ __len__ method was added, a SeqRecord always evaluated as True.
+
+ Note that in comparison, a Seq object will evaluate to False if it
+ has a zero length sequence.
+
+ WARNING: The SeqRecord may in future evaluate to False when its
+ sequence is of zero length (in order to better match the Seq
+ object behaviour)!
+ """
+ return True
+
+def _test():
+ """Run the Bio.SeqRecord module's doctests (PRIVATE).
+
+ This will try and locate the unit tests directory, and run the doctests
+ from there in order that the relative paths used in the examples work.
+ """
+ import doctest
+ import os
+ if os.path.isdir(os.path.join("..","Tests")) :
+ print "Runing doctests..."
+ cur_dir = os.path.abspath(os.curdir)
+ os.chdir(os.path.join("..","Tests"))
+ doctest.testmod()
+ os.chdir(cur_dir)
+ del cur_dir
+ print "Done"
+
+if __name__ == "__main__":
+ _test()
--- /dev/null
+# Copyright 2002 by Yves Bastide and Brad Chapman.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Functions to calculate assorted sequence checksums."""
+
+# crc32, crc64, gcg, and seguid
+# crc64 is adapted from BioPerl
+
+from binascii import crc32 as _crc32
+
+def crc32(seq) :
+ """Returns the crc32 checksum for a sequence (string or Seq object)"""
+ try :
+ #Assume its a Seq object
+ return _crc32(seq.tostring())
+ except AttributeError :
+ #Assume its a string
+ return _crc32(seq)
+
+def _init_table_h():
+ _table_h = []
+ for i in range(256):
+ l = i
+ part_h = 0
+ for j in range(8):
+ rflag = l & 1
+ l >>= 1
+ if part_h & 1: l |= (1L << 31)
+ part_h >>= 1L
+ if rflag: part_h ^= 0xd8000000L
+ _table_h.append(part_h)
+ return _table_h
+
+# Initialisation
+_table_h = _init_table_h()
+
+def crc64(s):
+ """Returns the crc64 checksum for a sequence (string or Seq object)"""
+ crcl = 0
+ crch = 0
+ for c in s:
+ shr = (crch & 0xFF) << 24
+ temp1h = crch >> 8
+ temp1l = (crcl >> 8) | shr
+ idx = (crcl ^ ord(c)) & 0xFF
+ crch = temp1h ^ _table_h[idx]
+ crcl = temp1l
+
+ return "CRC-%08X%08X" % (crch, crcl)
+
+
+def gcg(seq):
+ """Returns the GCG checksum (int) for a sequence (string or Seq object)
+
+ Given a nucleotide or amino-acid secuence (or any string),
+ returns the GCG checksum (int). Checksum used by GCG program.
+ seq type = str.
+ Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi
+ with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina.
+ All sequences are converted to uppercase """
+ index = checksum = 0
+ if type(seq)!=type("aa"):
+ seq=seq.tostring()
+ for char in seq:
+ index += 1
+ checksum += index * ord(char.upper())
+ if index == 57: index = 0
+ return checksum % 10000
+
+def seguid(seq):
+ """Returns the SEGUID (string) for a sequence (string or Seq object)
+
+ Given a nucleotide or amino-acid secuence (or any string),
+ returns the SEGUID string (A SEquence Globally Unique IDentifier).
+ seq type = str.
+ For more information about SEGUID, see:
+ http://bioinformatics.anl.gov/seguid/
+ DOI: 10.1002/pmic.200600032 """
+ try:
+ #Python 2.5 sha1 is in hashlib
+ import hashlib
+ m = hashlib.sha1()
+ except:
+ #For older versions
+ import sha
+ m = sha.new()
+ import base64
+ if type(seq)!=type("aa"):
+ seq=seq.tostring().upper()
+ else:
+ seq=seq.upper()
+ m.update(seq)
+ try:
+ #For Python 2.5
+ return base64.b64encode(m.digest()).rstrip("=")
+ except:
+ #For older versions
+ import os
+ #Note: Using os.linesep doesn't work on Windows,
+ #where os.linesep= "\r\n" but the encoded string
+ #contains "\n" but not "\r\n"
+ return base64.encodestring(m.digest()).replace("\n","").rstrip("=")
+
+if __name__ == "__main__" :
+ print "Quick self test"
+
+ str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ + "YCSSYAGSSTLVFGGGTKLTVL"
+
+ str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ + "YCCSYAGSSTWVFGGGTKLTVL"
+
+ assert crc64(str_light_chain_one) == crc64(str_light_chain_two)
+ assert 'CRC-44CAAD88706CC153' == crc64(str_light_chain_one)
+
+ assert 'BpBeDdcNUYNsdk46JoJdw7Pd3BI' == seguid(str_light_chain_one)
+ assert 'X5XEaayob1nZLOc7eVT9qyczarY' == seguid(str_light_chain_two)
+
+ print "Done"
--- /dev/null
+import math
+from CodonUsageIndices import SharpEcoliIndex
+from Bio import SeqIO # To parse a FASTA file
+
+CodonsDict = {'TTT':0, 'TTC':0, 'TTA':0, 'TTG':0, 'CTT':0,
+'CTC':0, 'CTA':0, 'CTG':0, 'ATT':0, 'ATC':0,
+'ATA':0, 'ATG':0, 'GTT':0, 'GTC':0, 'GTA':0,
+'GTG':0, 'TAT':0, 'TAC':0, 'TAA':0, 'TAG':0,
+'CAT':0, 'CAC':0, 'CAA':0, 'CAG':0, 'AAT':0,
+'AAC':0, 'AAA':0, 'AAG':0, 'GAT':0, 'GAC':0,
+'GAA':0, 'GAG':0, 'TCT':0, 'TCC':0, 'TCA':0,
+'TCG':0, 'CCT':0, 'CCC':0, 'CCA':0, 'CCG':0,
+'ACT':0, 'ACC':0, 'ACA':0, 'ACG':0, 'GCT':0,
+'GCC':0, 'GCA':0, 'GCG':0, 'TGT':0, 'TGC':0,
+'TGA':0, 'TGG':0, 'CGT':0, 'CGC':0, 'CGA':0,
+'CGG':0, 'AGT':0, 'AGC':0, 'AGA':0, 'AGG':0,
+'GGT':0, 'GGC':0, 'GGA':0, 'GGG':0}
+
+
+# this dictionary is used to know which codons encode the same AA.
+SynonymousCodons = {'CYS': ['TGT', 'TGC'], 'ASP': ['GAT', 'GAC'],
+'SER': ['TCT', 'TCG', 'TCA', 'TCC', 'AGC', 'AGT'],
+'GLN': ['CAA', 'CAG'], 'MET': ['ATG'], 'ASN': ['AAC', 'AAT'],
+'PRO': ['CCT', 'CCG', 'CCA', 'CCC'], 'LYS': ['AAG', 'AAA'],
+'STOP': ['TAG', 'TGA', 'TAA'], 'THR': ['ACC', 'ACA', 'ACG', 'ACT'],
+'PHE': ['TTT', 'TTC'], 'ALA': ['GCA', 'GCC', 'GCG', 'GCT'],
+'GLY': ['GGT', 'GGG', 'GGA', 'GGC'], 'ILE': ['ATC', 'ATA', 'ATT'],
+'LEU': ['TTA', 'TTG', 'CTC', 'CTT', 'CTG', 'CTA'], 'HIS': ['CAT', 'CAC'],
+'ARG': ['CGA', 'CGC', 'CGG', 'CGT', 'AGG', 'AGA'], 'TRP': ['TGG'],
+'VAL': ['GTA', 'GTC', 'GTG', 'GTT'], 'GLU': ['GAG', 'GAA'], 'TYR': ['TAT', 'TAC']}
+
+
+class CodonAdaptationIndex:
+ """A codon adaptaion index (CAI) implementation.
+
+ This class implements the codon adaptaion index (CAI) described by Sharp and
+ Li (Nucleic Acids Res. 1987 Feb 11;15(3):1281-95).
+
+ methods:
+
+ set_cai_index(Index):
+
+ This method sets-up an index to be used when calculating CAI for a gene.
+ Just pass a dictionary similar to the SharpEcoliIndex in CodonUsageIndices
+ module.
+
+ generate_index(FastaFile):
+
+ This method takes a location of a FastaFile and generates an index. This
+ index can later be used to calculate CAI of a gene.
+
+ cai_for_gene(DNAsequence):
+
+ This method uses the Index (either the one you set or the one you generated)
+ and returns the CAI for the DNA sequence.
+
+ print_index():
+ This method prints out the index you used.
+
+ NOTE - This implementation does not currently cope with alternative genetic
+ codes, only the synonymous codons in the standard table are considered.
+ """
+ def __init__(self):
+ self.index = {}
+ self.codon_count={}
+
+ # use this method with predefined CAI index
+ def set_cai_index(self, Index):
+ self.index = Index
+
+ def generate_index(self, FastaFile):
+ """Generate a codon usage index from a FASTA file of CDS sequences.
+
+ This method takes a location of a Fasta file containing CDS sequences
+ (which must all have a whole number of codons) and generates a codon
+ usage index. This index can later be used to calculate CAI of a gene.
+ """
+ # first make sure i am not overwriting an existing index:
+ if self.index != {} or self.codon_count!={}:
+ raise ValueError("an index has already been set or a codon count has been done. cannot overwrite either.")
+ # count codon occurances in the file.
+ self._count_codons(FastaFile)
+
+ # now to calculate the index we first need to sum the number of times
+ # synonymous codons were used all together.
+ for AA in SynonymousCodons.keys():
+ Sum=0.0
+ RCSU=[] # RCSU values are equal to CodonCount/((1/num of synonymous codons) * sum of all synonymous codons)
+
+ for codon in SynonymousCodons[AA]:
+ Sum += self.codon_count[codon]
+ # calculate the RSCU value for each of the codons
+ for codon in SynonymousCodons[AA]:
+ RCSU.append(self.codon_count[codon]/((1.0/len(SynonymousCodons[AA]))*Sum))
+ # now generate the index W=RCSUi/RCSUmax:
+ RCSUmax = max(RCSU)
+ for i in range(len(SynonymousCodons[AA])):
+ self.index[SynonymousCodons[AA][i]]= RCSU[i]/RCSUmax
+
+
+ def cai_for_gene(self, DNAsequence):
+ """Calculate the CAI (float) for the provided DNA sequence (string).
+
+ This method uses the Index (either the one you set or the one you generated)
+ and returns the CAI for the DNA sequence.
+ """
+ caiValue = 0
+ LengthForCai = 0
+ # if no index is set or generated, the default SharpEcoliIndex will be used.
+ if self.index=={}:
+ self.set_cai_index(SharpEcoliIndex)
+
+ if DNAsequence.islower():
+ DNAsequence = DNAsequence.upper()
+ for i in range (0,len(DNAsequence),3):
+ codon = DNAsequence[i:i+3]
+ if codon in self.index:
+ if codon!='ATG' and codon!= 'TGG': #these two codons are always one, exclude them.
+ caiValue += math.log(self.index[codon])
+ LengthForCai += 1
+ elif codon not in ['TGA','TAA', 'TAG']: # some indices you will use may not include stop codons.
+ raise TypeError("illegal codon in sequence: %s.\n%s" % (codon, self.index))
+ return math.exp(caiValue*(1.0/(LengthForCai-1)))
+
+ def _count_codons(self, FastaFile):
+ handle = open(FastaFile, 'r')
+
+ # make the codon dictionary local
+ self.codon_count = CodonsDict.copy()
+
+ # iterate over sequence and count all the codons in the FastaFile.
+ for cur_record in SeqIO.parse(handle, "fasta") :
+ # make sure the sequence is lower case
+ if str(cur_record.seq).islower():
+ DNAsequence = str(cur_record.seq).upper()
+ else:
+ DNAsequence = str(cur_record.seq)
+ for i in range(0,len(DNAsequence),3):
+ codon = DNAsequence[i:i+3]
+ if codon in self.codon_count:
+ self.codon_count[codon] += 1
+ else:
+ raise TypeError("illegal codon %s in gene: %s" % (codon, cur_record.id))
+ handle.close()
+
+ # this just gives the index when the objects is printed.
+ def print_index (self):
+ """This method prints out the index you used."""
+ X=self.index.keys()
+ X.sort()
+ for i in X:
+ print "%s\t%.3f" %(i, self.index[i])
+
--- /dev/null
+# Copyright Yair Benita Y.Benita@pharm.uu.nl
+# Biopython (http://biopython.org) license applies
+
+# sharp Ecoli index for codon adaption index.
+# from Sharp & Li, Nucleic Acids Res. 1987
+SharpEcoliIndex = {
+'GCA':0.586, 'GCC':0.122, 'GCG':0.424, 'GCT':1, 'AGA':0.004, 'AGG':0.002, 'CGA':0.004,
+'CGC':0.356, 'CGG':0.004, 'CGT':1, 'AAC':1, 'AAT':0.051, 'GAC':1, 'GAT':0.434, 'TGC':1,
+'TGT':0.5, 'CAA':0.124, 'CAG':1, 'GAA':1, 'GAG':0.259, 'GGA':0.01, 'GGC':0.724, 'GGG':0.019,
+'GGT':1, 'CAC':1, 'CAT':0.291, 'ATA':0.003, 'ATC':1, 'ATT':0.185, 'CTA':0.007, 'CTC':0.037,
+'CTG':1, 'CTT':0.042, 'TTA':0.02, 'TTG':0.02, 'AAA':1, 'AAG':0.253, 'ATG':1, 'TTC':1, 'TTT':0.296,
+'CCA':0.135, 'CCC':0.012, 'CCG':1, 'CCT':0.07, 'AGC':0.41, 'AGT':0.085, 'TCA':0.077, 'TCC':0.744,
+'TCG':0.017, 'TCT':1, 'ACA':0.076, 'ACC':1,'ACG':0.099, 'ACT':0.965, 'TGG':1, 'TAC':1, 'TAT':0.239,
+'GTA':0.495, 'GTC':0.066,'GTG':0.221, 'GTT':1}
--- /dev/null
+# Copyright Yair Benita Y.Benita@pharm.uu.nl
+# Biopython (http://biopython.org) license applies
+
+"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
+
+pK values and the methos are taken from:
+
+* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
+J.-Ch., Frutiger, S. & Hochstrasser, D.F.
+The focusing positions of polypeptides in immobilized pH gradients can be predicted
+from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
+
+* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
+Reference points for comparisons of two-dimensional maps of proteins from
+different human cell types defined in a pH scale where isoelectric points correlate
+with polypeptide compositions. Electrophoresis 1994, 15, 529-539.
+
+I designed the algorithm according to a note by David L. Tabb, available at:
+http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf
+
+"""
+
+positive_pKs = { 'Nterm': 7.5, 'K': 10.0, 'R': 12.0, 'H':5.98 }
+negative_pKs = { 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C':9.0, 'Y':10.0 }
+pKcterminal= {'D':4.55, 'E':4.75}
+pKnterminal = {'A':7.59, 'M':7.0, 'S':6.93, 'P':8.36, 'T':6.82, 'V':7.44, 'E':7.7}
+charged_aas = ('K', 'R', 'H', 'D', 'E', 'C', 'Y')
+
+# access this module through ProtParam.ProteinAnalysis class.
+# first make a ProteinAnalysis object and then call its isoelectric_point method.
+class IsoelectricPoint:
+ def __init__(self, ProteinSequence, AminoAcidsContent):
+ self.sequence = ProteinSequence
+ self.charged_aas_content = self._select_charged(AminoAcidsContent)
+
+ # This function creates a dictionary with the contents of each charged aa,
+ # plus Cterm and Nterm.
+ def _select_charged(self, AminoAcidsContent):
+ charged = {}
+ for aa in charged_aas:
+ charged[aa] = float(AminoAcidsContent[aa])
+ charged['Nterm'] = 1.0
+ charged['Cterm'] = 1.0
+ return charged
+
+ #This function calculates the total charge of the protein at a given pH.
+ def _chargeR(self, pH, pos_pKs, neg_pKs):
+ PositiveCharge = 0.0
+ for aa, pK in pos_pKs.iteritems():
+ CR = 10**(pK-pH)
+ partial_charge = CR/(CR+1.0)
+ PositiveCharge += self.charged_aas_content[aa] * partial_charge
+
+ NegativeCharge = 0.0
+ for aa, pK in neg_pKs.iteritems():
+ CR = 10**(pH-pK)
+ partial_charge = CR/(CR+1.0)
+ NegativeCharge += self.charged_aas_content[aa] * partial_charge
+
+ return PositiveCharge - NegativeCharge
+
+ # This is the action function, it tries different pH until the charge of the protein is 0 (or close).
+ def pi(self):
+ pos_pKs = dict(positive_pKs)
+ neg_pKs = dict(negative_pKs)
+ nterm = self.sequence[0]
+ cterm = self.sequence[-1]
+ if nterm in pKnterminal.keys():
+ pos_pKs['Nterm'] = pKnterminal[nterm]
+ if cterm in pKcterminal.keys():
+ neg_pKs['Cterm'] = pKcterminal[cterm]
+
+ # Bracket between pH1 and pH2
+ pH = 7.0
+ Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+ if Charge > 0.0:
+ pH1 = pH
+ Charge1 = Charge
+ while Charge1 > 0.0:
+ pH = pH1 + 1.0
+ Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+ if Charge > 0.0:
+ pH1 = pH
+ Charge1 = Charge
+ else:
+ pH2 = pH
+ Charge2 = Charge
+ break
+ else:
+ pH2 = pH
+ Charge2 = Charge
+ while Charge2 < 0.0:
+ pH = pH2 - 1.0
+ Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+ if Charge < 0.0:
+ pH2 = pH
+ Charge2 = Charge
+ else:
+ pH1 = pH
+ Charge1 = Charge
+ break
+
+ # Bisection
+ while pH2 - pH1 > 0.0001 and Charge!=0.0:
+ pH = (pH1 + pH2) / 2.0
+ Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+ if Charge > 0.0:
+ pH1 = pH
+ Charge1 = Charge
+ else:
+ pH2 = pH
+ Charge2 = Charge
+
+ return pH
--- /dev/null
+# Copyright 2004-2008 by Sebastian Bassi.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Calculate the thermodynamic melting temperatures of nucleotide sequences."""
+
+import math
+def Tm_staluc(s,dnac=50,saltc=50,rna=0):
+ """Returns DNA/DNA tm using nearest neighbor thermodynamics.
+
+ dnac is DNA concentration [nM]
+ saltc is salt concentration [mM].
+ rna=0 is for DNA/DNA (default), for RNA, rna should be 1.
+
+ Sebastian Bassi <sbassi@genesdigitales.com>"""
+
+ #Credits:
+ #Main author: Sebastian Bassi <sbassi@genesdigitales.com>
+ #Overcount function: Greg Singer <singerg@tcd.ie>
+ #Based on the work of Nicolas Le Novere <lenov@ebi.ac.uk> Bioinformatics.
+ #17:1226-1227(2001)
+
+ #This function returns better results than EMBOSS DAN because it uses
+ #updated thermodynamics values and takes into account inicialization
+ #parameters from the work of SantaLucia (1998).
+
+ #Things to do:
+ #+Detect complementary sequences. Change K according to result.
+ #+Add support for heteroduplex (see Sugimoto et al. 1995).
+ #+Correction for Mg2+. Now supports only monovalent ions.
+ #+Put thermodinamics table in a external file for users to change at will
+ #+Add support for danglings ends (see Le Novele. 2001) and mismatches.
+
+ dh = 0 #DeltaH. Enthalpy
+ ds = 0 #deltaS Entropy
+
+ def tercorr(stri):
+ deltah = 0
+ deltas = 0
+ if rna==0:
+ #DNA/DNA
+ #Allawi and SantaLucia (1997). Biochemistry 36 : 10581-10594
+ if stri.startswith('G') or stri.startswith('C'):
+ deltah -= 0.1
+ deltas += 2.8
+ elif stri.startswith('A') or stri.startswith('T'):
+ deltah -= 2.3
+ deltas -= 4.1
+ if stri.endswith('G') or stri.endswith('C'):
+ deltah -= 0.1
+ deltas += 2.8
+ elif stri.endswith('A') or stri.endswith('T'):
+ deltah -= 2.3
+ deltas -= 4.1
+ dhL = dh + deltah
+ dsL = ds + deltas
+ return dsL,dhL
+ elif rna==1:
+ #RNA
+ if stri.startswith('G') or stri.startswith('C'):
+ deltah -= 3.61
+ deltas -= 1.5
+ elif stri.startswith('A') or stri.startswith('T') or \
+ stri.startswith('U'):
+ deltah -= 3.72
+ deltas += 10.5
+ if stri.endswith('G') or stri.endswith('C'):
+ deltah -= 3.61
+ deltas -= 1.5
+ elif stri.endswith('A') or stri.endswith('T') or \
+ stri.endswith('U'):
+ deltah -= 3.72
+ deltas += 10.5
+ dhL = dh + deltah
+ dsL = ds + deltas
+ # print "delta h=",dhL
+ return dsL,dhL
+
+ def overcount(st,p):
+ """Returns how many p are on st, works even for overlapping"""
+ ocu = 0
+ x = 0
+ while 1:
+ try:
+ i = st.index(p,x)
+ except ValueError:
+ break
+ ocu += 1
+ x = i + 1
+ return ocu
+
+ R = 1.987 # universal gas constant in Cal/degrees C*Mol
+ sup = s.upper()
+ vsTC,vh = tercorr(sup)
+ vs = vsTC
+
+ k = (dnac/4.0)*1e-9
+ #With complementary check on, the 4.0 should be changed to a variable.
+
+ if rna==0:
+ #DNA/DNA
+ #Allawi and SantaLucia (1997). Biochemistry 36 : 10581-10594
+ vh = vh + (overcount(sup,"AA"))*7.9 + (overcount(sup,"TT"))*\
+ 7.9 + (overcount(sup,"AT"))*7.2 + (overcount(sup,"TA"))*7.2 \
+ + (overcount(sup,"CA"))*8.5 + (overcount(sup,"TG"))*8.5 + \
+ (overcount(sup,"GT"))*8.4 + (overcount(sup,"AC"))*8.4
+ vh = vh + (overcount(sup,"CT"))*7.8+(overcount(sup,"AG"))*\
+ 7.8 + (overcount(sup,"GA"))*8.2 + (overcount(sup,"TC"))*8.2
+ vh = vh + (overcount(sup,"CG"))*10.6+(overcount(sup,"GC"))*\
+ 9.8 + (overcount(sup,"GG"))*8 + (overcount(sup,"CC"))*8
+ vs = vs + (overcount(sup,"AA"))*22.2+(overcount(sup,"TT"))*\
+ 22.2 + (overcount(sup,"AT"))*20.4 + (overcount(sup,"TA"))*21.3
+ vs = vs + (overcount(sup,"CA"))*22.7+(overcount(sup,"TG"))*\
+ 22.7 + (overcount(sup,"GT"))*22.4 + (overcount(sup,"AC"))*22.4
+ vs = vs + (overcount(sup,"CT"))*21.0+(overcount(sup,"AG"))*\
+ 21.0 + (overcount(sup,"GA"))*22.2 + (overcount(sup,"TC"))*22.2
+ vs = vs + (overcount(sup,"CG"))*27.2+(overcount(sup,"GC"))*\
+ 24.4 + (overcount(sup,"GG"))*19.9 + (overcount(sup,"CC"))*19.9
+ ds = vs
+ dh = vh
+
+ else:
+ #RNA/RNA hybridisation of Xia et al (1998)
+ #Biochemistry 37: 14719-14735
+ vh = vh+(overcount(sup,"AA"))*6.82+(overcount(sup,"TT"))*6.6+\
+ (overcount(sup,"AT"))*9.38 + (overcount(sup,"TA"))*7.69+\
+ (overcount(sup,"CA"))*10.44 + (overcount(sup,"TG"))*10.5+\
+ (overcount(sup,"GT"))*11.4 + (overcount(sup,"AC"))*10.2
+ vh = vh + (overcount(sup,"CT"))*10.48 + (overcount(sup,"AG"))\
+ *7.6+(overcount(sup,"GA"))*12.44+(overcount(sup,"TC"))*13.3
+ vh = vh + (overcount(sup,"CG"))*10.64 + (overcount(sup,"GC"))\
+ *14.88+(overcount(sup,"GG"))*13.39+(overcount(sup,"CC"))*12.2
+ vs = vs + (overcount(sup,"AA"))*19.0 + (overcount(sup,"TT"))*\
+ 18.4+(overcount(sup,"AT"))*26.7+(overcount(sup,"TA"))*20.5
+ vs = vs + (overcount(sup,"CA"))*26.9 + (overcount(sup,"TG"))*\
+ 27.8 + (overcount(sup,"GT"))*29.5 + (overcount(sup,"AC"))*26.2
+ vs = vs + (overcount(sup,"CT"))*27.1 + (overcount(sup,"AG"))*\
+ 19.2 + (overcount(sup,"GA"))*32.5 + (overcount(sup,"TC"))*35.5
+ vs = vs + (overcount(sup,"CG"))*26.7 + (overcount(sup,"GC"))\
+ *36.9 + (overcount(sup,"GG"))*32.7 + (overcount(sup,"CC"))*29.7
+ ds = vs
+ dh = vh
+
+ ds = ds-0.368*(len(s)-1)*math.log(saltc/1e3)
+ tm = ((1000* (-dh))/(-ds+(R * (math.log(k)))))-273.15
+ # print "ds="+str(ds)
+ # print "dh="+str(dh)
+ return tm
+
+if __name__ == "__main__" :
+ print "Quick self test"
+ assert Tm_staluc('CAGTCAGTACGTACGTGTACTGCCGTA') == 59.865612727457972
+ assert Tm_staluc('CAGTCAGTACGTACGTGTACTGCCGTA',rna=1) == 68.141611264576682
+ print "Done"
--- /dev/null
+# Copyright Yair Benita Y.Benita@pharm.uu.nl
+# Biopython (http://biopython.org) license applies
+
+import sys
+import ProtParamData, IsoelectricPoint
+from ProtParamData import kd # Added by Iddo to enable the gravy method
+from Bio.Seq import Seq
+from Bio.Alphabet import IUPAC
+from Bio.Data import IUPACData
+#from BioModule import
+
+class ProteinAnalysis:
+ """
+ This class contains methods for protein analysis. The class init method takes
+ only one argument, the protein sequence as a string and build a sequence
+ object using the Bio.Seq module. This is done just to make sure the sequence
+ is a protein sequence and not anything else.
+
+ methods:
+
+ count_amino_acids:
+
+ Simply counts the number times an amino acid is repeated in the protein
+ sequence. Returns a dictionary {AminoAcid:Number} and also stores the
+ dictionary in self.amino_acids_content.
+
+ get_amino_acids_percent:
+
+ The same as count_amino_acids only returns the Number in percentage of entire
+ sequence. Returns a dictionary and stores the dictionary in
+ self.amino_acids_content_percent.
+
+ molecular_weight:
+ Calculates the molecular weight of a protein.
+
+ aromaticity:
+
+ Calculates the aromaticity value of a protein according to Lobry, 1994. It is
+ simply the relative frequency of Phe+Trp+Tyr.
+
+
+ instability_index:
+
+ Implementation of the method of Guruprasad et al. (Protein Engineering
+ 4:155-161,1990). This method tests a protein for stability. Any value above 40
+ means the protein is unstable (=has a short half life).
+
+ flexibility:
+ Implementation of the flexibility method of Vihinen et al. (Proteins. 1994 Jun;19(2):141-9).
+
+ isoelectric_point:
+ This method uses the module IsoelectricPoint to calculate the pI of a protein.
+
+ secondary_structure_fraction:
+ This methods returns a list of the fraction of amino acids which tend to be in Helix, Turn or Sheet.
+ Amino acids in helix: V, I, Y, F, W, L.
+ Amino acids in Turn: N, P, G, S.
+ Amino acids in sheet: E, M, A, L.
+ The list contains 3 values: [Helix, Turn, Sheet].
+
+
+ protein_scale(Scale, WindwonSize, Edge):
+
+ An amino acid scale is defined by a numerical value assigned to each type of
+ amino acid. The most frequently used scales are the hydrophobicity or
+ hydrophilicity scales and the secondary structure conformational parameters
+ scales, but many other scales exist which are based on different chemical and
+ physical properties of the amino acids. You can set several parameters that
+ control the computation of a scale profile, such as the window size and the
+ window edge relative weight value. WindowSize: The window size is the length
+ of the interval to use for the profile computation. For a window size n, we
+ use the i- ( n-1)/2 neighboring residues on each side of residue it compute
+ the score for residue i. The score for residue is the sum of the scale values
+ for these amino acids, optionally weighted according to their position in the
+ window. Edge: The central amino acid of the window always has a weight of 1.
+ By default, the amino acids at the remaining window positions have the same
+ weight, but you can make the residue at the center of the window have a
+ larger weight than the others by setting the edge value for the residues at
+ the beginning and end of the interval to a value between 0 and 1. For
+ instance, for Edge=0.4 and a window size of 5 the weights will be: 0.4, 0.7,
+ 1.0, 0.7, 0.4. The method returns a list of values which can be plotted to
+ view the change along a protein sequence. Many scales exist. Just add your
+ favorites to the ProtParamData modules.
+ """
+ def __init__(self, ProtSequence):
+ if ProtSequence.islower():
+ self.sequence = Seq(ProtSequence.upper(), IUPAC.protein)
+ else:
+ self.sequence = Seq(ProtSequence, IUPAC.protein)
+ self.amino_acids_content = None
+ self.amino_acids_percent = None
+ self.length = len(self.sequence)
+
+ def count_amino_acids(self):
+ ProtDic = dict([ (k, 0) for k in IUPACData.protein_letters])
+ for i in ProtDic.keys():
+ ProtDic[i]=self.sequence.count(i)
+ self.amino_acids_content = ProtDic
+ return ProtDic
+
+ """Calculate the amino acid content in percents.
+ input is the dictionary from CountAA.
+ output is a dictionary with AA as keys."""
+ def get_amino_acids_percent(self):
+ if not self.amino_acids_content:
+ self.count_amino_acids()
+
+ PercentAA = {}
+ for i in self.amino_acids_content.keys():
+ if self.amino_acids_content[i] > 0:
+ PercentAA[i]=self.amino_acids_content[i]/float(self.length)
+ else:
+ PercentAA[i] = 0
+ self.amino_acids_percent = PercentAA
+ return PercentAA
+
+ # Calculate MW from Protein sequence
+ # Calculate MW from Protein sequence
+ def molecular_weight (self):
+ # make local dictionary for speed
+ MwDict = {}
+ # remove a molecule of water from the amino acid weight.
+ for i in IUPACData.protein_weights.keys():
+ MwDict[i] = IUPACData.protein_weights[i] - 18.02
+ MW = 18.02 # add just one water molecule for the whole sequence.
+ for i in self.sequence:
+ MW += MwDict[i]
+ return MW
+
+ # calculate the aromaticity according to Lobry, 1994.
+ # Arom=sum of relative frequency of Phe+Trp+Tyr
+ def aromaticity(self):
+ if not self.amino_acids_percent:
+ self.get_amino_acids_percent()
+
+ Arom= self.amino_acids_percent['Y']+self.amino_acids_percent['W']+self.amino_acids_percent['F']
+ return Arom
+
+ # a function to calculate the instability index according to:
+ # Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
+ def instability_index(self):
+ #make the dictionary local for speed.
+ DIWV=ProtParamData.DIWV.copy()
+ score=0.0
+ for i in range(self.length - 1):
+ DiPeptide=DIWV[self.sequence[i]][self.sequence[i+1]]
+ score += DiPeptide
+ return (10.0/self.length) * score
+
+ # Calculate the flexibility according to Vihinen, 1994.
+ # No argument to change window size because parameters are specific for a window=9.
+ # the parameters used are optimized for determining the flexibility.
+ def flexibility(self):
+ Flex = ProtParamData.Flex.copy()
+ Window=9
+ Weights=[0.25,0.4375,0.625,0.8125,1]
+ List=[]
+ for i in range(self.length - Window):
+ SubSeq=self.sequence[i:i+Window]
+ score = 0.0
+ for j in range(Window/2):
+ score += (Flex[SubSeq[j]]+Flex[SubSeq[Window-j-1]]) * Weights[j]
+ score += Flex[SubSeq[Window/2+1]]
+ List.append(score/5.25)
+ return List
+
+ # calculate the gravy according to kyte and doolittle.
+ def gravy(self):
+ ProtGravy=0.0
+ for i in self.sequence:
+ ProtGravy += kd[i]
+
+ return ProtGravy/self.length
+
+ # this method is used to make a list of relative weight of the
+ # window edges compared to the window center. The weights are linear.
+ # it actually generates half a list. For a window of size 9 and edge 0.4
+ # you get a list of [0.4, 0.55, 0.7, 0.85].
+ def _weight_list(self, window, edge):
+ unit = ((1.0-edge)/(window-1))*2
+ list = [0.0]*(window/2)
+ for i in range(window/2):
+ list[i] = edge + unit * i
+ return list
+
+ # this method allows you to compute and represent the profile produced
+ # by any amino acid scale on a selected protein.
+ # Similar to expasy's ProtScale: http://www.expasy.org/cgi-bin/protscale.pl
+ # The weight list returns only one tail. If the list should be [0.4,0.7,1.0,0.7,0.4]
+ # what you actually get from _weights_list is [0.4,0.7]. The correct calculation is done
+ # in the loop.
+ def protein_scale(self, ParamDict, Window, Edge=1.0):
+ # generate the weights
+ weight = self._weight_list(Window,Edge)
+ list = []
+ # the score in each Window is divided by the sum of weights
+ sum_of_weights = 0.0
+ for i in weight: sum_of_weights += i
+ # since the weight list is one sided:
+ sum_of_weights = sum_of_weights*2+1
+
+ for i in range(self.length-Window+1):
+ subsequence = self.sequence[i:i+Window]
+ score = 0.0
+ for j in range(Window/2):
+ # walk from the outside of the Window towards the middle.
+ # Iddo: try/except clauses added to avoid raising an exception on a non-standad amino acid
+ try:
+ score += weight[j] * ParamDict[subsequence[j]] + weight[j] * ParamDict[subsequence[Window-j-1]]
+ except KeyError:
+ sys.stderr.write('warning: %s or %s is not a standard amino acid.\n' %
+ (subsequence[j],subsequence[Window-j-1]))
+
+ # Now add the middle value, which always has a weight of 1.
+ if subsequence[Window/2] in ParamDict:
+ score += ParamDict[subsequence[Window/2]]
+ else:
+ sys.stderr.write('warning: %s is not a standard amino acid.\n' % (subsequence[Window/2]))
+
+ list.append(score/sum_of_weights)
+ return list
+
+ # calculate the isoelectric point.
+ def isoelectric_point(self):
+ if not self.amino_acids_content:
+ self.count_amino_acids()
+ X = IsoelectricPoint.IsoelectricPoint(self.sequence, self.amino_acids_content)
+ return X.pi()
+
+ # calculate fraction of helix, turn and sheet
+ def secondary_structure_fraction (self):
+ if not self.amino_acids_percent:
+ self.get_amino_acids_percent()
+ Helix = self.amino_acids_percent['V'] + self.amino_acids_percent['I'] + self.amino_acids_percent['Y'] + self.amino_acids_percent['F'] + self.amino_acids_percent['W'] + self.amino_acids_percent['L']
+ Turn = self.amino_acids_percent['N'] + self.amino_acids_percent['P'] + self.amino_acids_percent['G'] + self.amino_acids_percent['S']
+ Sheet = self.amino_acids_percent['E'] + self.amino_acids_percent['M'] + self.amino_acids_percent['A'] + self.amino_acids_percent['L']
+ return Helix, Turn, Sheet
+
+#---------------------------------------------------------#
+"""
+X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
+print X.count_amino_acids()
+print X.get_amino_acids_percent()
+print X.molecular_weight()
+print X.aromaticity()
+print X.instability_index()
+print X.flexibility()
+print X.pi()
+print X.secondary_structure_fraction()
+print X.protein_scale(ProtParamData.kd, 9, 0.4)
+"""
--- /dev/null
+# This module contains indices to be used with ProtParam
+
+# Kyte & Doolittle index of hydrophobicity
+kd = { 'A': 1.8,'R':-4.5,'N':-3.5,'D':-3.5,'C': 2.5,
+ 'Q':-3.5,'E':-3.5,'G':-0.4,'H':-3.2,'I': 4.5,
+ 'L': 3.8,'K':-3.9,'M': 1.9,'F': 2.8,'P':-1.6,
+ 'S':-0.8,'T':-0.7,'W':-0.9,'Y':-1.3,'V': 4.2 }
+
+# Flexibility
+# Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
+Flex= {'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,
+ 'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
+ 'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
+ 'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
+ 'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929}
+
+# Hydrophilicity
+# 1 Hopp & Wood
+# Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
+hw = { 'A':-0.5,'R':3.0, 'N':0.2, 'D':3.0, 'C':-1.0,
+ 'Q':0.2, 'E':3.0, 'G':0.0, 'H':-0.5,'I':-1.8,
+ 'L':-1.8,'K':3.0, 'M':-1.3,'F':-2.5,'P':0.0,
+ 'S':0.3, 'T':-0.4,'W':-3.4,'Y':-2.3,'V':-1.5 }
+
+# Surface accessibility
+# 1 Emini Surface fractional probability
+em = { 'A':0.815,'R':1.475,'N':1.296,'D':1.283,'C':0.394,
+ 'Q':1.348,'E':1.445,'G':0.714,'H':1.180,'I':0.603,
+ 'L':0.603,'K':1.545,'M':0.714,'F':0.695,'P':1.236,
+ 'S':1.115,'T':1.184,'W':0.808,'Y':1.089,'V':0.606 }
+
+# 2 Janin Interior to surface transfer energy scale
+ja = { 'A': 0.28,'R':-1.14,'N':-0.55,'D':-0.52,'C': 0.97,
+ 'Q':-0.69,'E':-1.01,'G': 0.43,'H':-0.31,'I': 0.60,
+ 'L': 0.60,'K':-1.62,'M': 0.43,'F': 0.46,'P':-0.42,
+ 'S':-0.19,'T':-0.32,'W': 0.29,'Y':-0.15,'V': 0.60 }
+
+
+# A two dimentional dictionary for calculating the instability index.
+# Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
+# It is based on dipeptide values therefore the vale for the dipeptide DG is DIWV['D']['G'].
+# I know this looks ugly but i can't think of a better way to display it.
+DIWV = {'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60, 'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0, 'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0, 'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0},'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26, 'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0, 'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0}, 'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0, 'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54, 'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0}, 'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0, 'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0, 'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49, 'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0, 'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49}, 'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601}, 'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34, 'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0, 'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0, 'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0, 'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68, 'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0, 'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94}, 'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0, 'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0, 'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60, 'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28, 'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0, 'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54, 'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68}, 'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26, 'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0}, 'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0, 'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0, 'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0, 'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0}, 'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26, 'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0, 'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54}, 'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54, 'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0, 'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0, 'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54, 'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0}, 'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0, 'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26, 'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0}, 'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34, 'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28, 'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54}, 'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0, 'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0, 'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03, 'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0, 'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0}, 'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0, 'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68, 'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34, 'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0, 'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03, 'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0, 'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0, 'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54}, 'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68, 'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34, 'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0, 'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91, 'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34}}
\ No newline at end of file
--- /dev/null
+#!/usr/bin/env python
+# Created: Wed May 29 08:07:18 2002
+# thomas@cbs.dtu.dk, Cecilia.Alsmark@ebc.uu.se
+# Copyright 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Miscellaneous functions for dealing with sequences."""
+
+import re, time
+from Bio import SeqIO
+from Bio import Translate
+from Bio.Seq import Seq
+from Bio import Alphabet
+from Bio.Alphabet import IUPAC
+from Bio.Data import IUPACData, CodonTable
+
+
+######################################
+# DNA
+######################
+# {{{
+
+def reverse(seq):
+ """Reverse the sequence. Works on string sequences.
+
+ e.g.
+ >>> reverse("ACGGT")
+ 'TGGCA'
+
+ """
+ r = list(seq)
+ r.reverse()
+ return ''.join(r)
+
+def GC(seq):
+ """Calculates G+C content, returns the percentage (float between 0 and 100).
+
+ Copes mixed case seuqneces, and with the ambiguous nucleotide S (G or C)
+ when counting the G and C content. The percentage is calculated against
+ the full length, e.g.:
+
+ >>> from Bio.SeqUtils import GC
+ >>> GC("ACTGN")
+ 40.0
+
+ Note that this will return zero for an empty sequence.
+ """
+ try :
+ gc = sum(map(seq.count,['G','C','g','c','S','s']))
+ return gc*100.0/len(seq)
+ except ZeroDivisionError :
+ return 0.0
+
+
+def GC123(seq):
+ """Calculates total G+C content plus first, second and third positions.
+
+ Returns a tuple of four floats (percentages between 0 and 100) for the
+ entire sequence, and the three codon positions. e.g.
+
+ >>> from Bio.SeqUtils import GC123
+ >>> GC123("ACTGTN")
+ (40.0, 50.0, 50.0, 0.0)
+
+ Copes with mixed case sequences, but does NOT deal with ambiguous
+ nucleotides.
+ """
+ d= {}
+ for nt in ['A','T','G','C']:
+ d[nt] = [0,0,0]
+
+ for i in range(0,len(seq),3):
+ codon = seq[i:i+3]
+ if len(codon) <3: codon += ' '
+ for pos in range(0,3):
+ for nt in ['A','T','G','C']:
+ if codon[pos] == nt or codon[pos] == nt.lower():
+ d[nt][pos] += 1
+ gc = {}
+ gcall = 0
+ nall = 0
+ for i in range(0,3):
+ try:
+ n = d['G'][i] + d['C'][i] +d['T'][i] + d['A'][i]
+ gc[i] = (d['G'][i] + d['C'][i])*100.0/n
+ except:
+ gc[i] = 0
+
+ gcall = gcall + d['G'][i] + d['C'][i]
+ nall = nall + n
+
+ gcall = 100.0*gcall/nall
+ return gcall, gc[0], gc[1], gc[2]
+
+def GC_skew(seq, window = 100):
+ """Calculates GC skew (G-C)/(G+C) for multuple windows along the sequence.
+
+ Returns a list of ratios (floats), controlled by the length of the sequence
+ and the size of the window.
+
+ Does NOT look at any ambiguous nucleotides.
+ """
+ # 8/19/03: Iddo: added lowercase
+ values = []
+ for i in range(0, len(seq), window):
+ s = seq[i: i + window]
+ g = s.count('G') + s.count('g')
+ c = s.count('C') + s.count('c')
+ skew = (g-c)/float(g+c)
+ values.append(skew)
+ return values
+
+from math import pi, sin, cos, log
+def xGC_skew(seq, window = 1000, zoom = 100,
+ r = 300, px = 100, py = 100):
+ """Calculates and plots normal and accumulated GC skew (GRAPHICS !!!)."""
+ from Tkinter import Scrollbar, Canvas, BOTTOM, BOTH, ALL, \
+ VERTICAL, HORIZONTAL, RIGHT, LEFT, X, Y
+ yscroll = Scrollbar(orient = VERTICAL)
+ xscroll = Scrollbar(orient = HORIZONTAL)
+ canvas = Canvas(yscrollcommand = yscroll.set,
+ xscrollcommand = xscroll.set, background = 'white')
+ win = canvas.winfo_toplevel()
+ win.geometry('700x700')
+
+ yscroll.config(command = canvas.yview)
+ xscroll.config(command = canvas.xview)
+ yscroll.pack(side = RIGHT, fill = Y)
+ xscroll.pack(side = BOTTOM, fill = X)
+ canvas.pack(fill=BOTH, side = LEFT, expand = 1)
+ canvas.update()
+
+ X0, Y0 = r + px, r + py
+ x1, x2, y1, y2 = X0 - r, X0 + r, Y0 -r, Y0 + r
+
+ ty = Y0
+ canvas.create_text(X0, ty, text = '%s...%s (%d nt)' % (seq[:7], seq[-7:], len(seq)))
+ ty +=20
+ canvas.create_text(X0, ty, text = 'GC %3.2f%%' % (GC(seq)))
+ ty +=20
+ canvas.create_text(X0, ty, text = 'GC Skew', fill = 'blue')
+ ty +=20
+ canvas.create_text(X0, ty, text = 'Accumulated GC Skew', fill = 'magenta')
+ ty +=20
+ canvas.create_oval(x1,y1, x2, y2)
+
+ acc = 0
+ start = 0
+ for gc in GC_skew(seq, window):
+ r1 = r
+ acc+=gc
+ # GC skew
+ alpha = pi - (2*pi*start)/len(seq)
+ r2 = r1 - gc*zoom
+ x1 = X0 + r1 * sin(alpha)
+ y1 = Y0 + r1 * cos(alpha)
+ x2 = X0 + r2 * sin(alpha)
+ y2 = Y0 + r2 * cos(alpha)
+ canvas.create_line(x1,y1,x2,y2, fill = 'blue')
+ # accumulated GC skew
+ r1 = r - 50
+ r2 = r1 - acc
+ x1 = X0 + r1 * sin(alpha)
+ y1 = Y0 + r1 * cos(alpha)
+ x2 = X0 + r2 * sin(alpha)
+ y2 = Y0 + r2 * cos(alpha)
+ canvas.create_line(x1,y1,x2,y2, fill = 'magenta')
+
+ canvas.update()
+ start += window
+
+ canvas.configure(scrollregion = canvas.bbox(ALL))
+
+def molecular_weight(seq):
+ """Calculate the molecular weight of a DNA sequence."""
+ if type(seq) == type(''): seq = Seq(seq, IUPAC.unambiguous_dna)
+ weight_table = IUPACData.unambiguous_dna_weights
+ #TODO, use a generator expession once we drop Python 2.3?
+ #e.g. return sum(weight_table[x] for x in seq)
+ total = 0
+ for x in seq:
+ total += weight_table[x]
+ return total
+
+def nt_search(seq, subseq):
+ """Search for a DNA subseq in sequence.
+
+ use ambiguous values (like N = A or T or C or G, R = A or G etc.)
+ searches only on forward strand
+ """
+ pattern = ''
+ for nt in subseq:
+ value = IUPACData.ambiguous_dna_values[nt]
+ if len(value) == 1:
+ pattern += value
+ else:
+ pattern += '[%s]' % value
+
+ pos = -1
+ result = [pattern]
+ l = len(seq)
+ while True:
+ pos+=1
+ s = seq[pos:]
+ m = re.search(pattern, s)
+ if not m: break
+ pos += int(m.start(0))
+ result.append(pos)
+ return result
+
+# }}}
+
+######################################
+# Protein
+######################
+# {{{
+
+# temporary hack for exception free translation of "dirty" DNA
+# should be moved to ???
+
+class ProteinX(Alphabet.ProteinAlphabet):
+ letters = IUPACData.extended_protein_letters + "X"
+
+proteinX = ProteinX()
+
+class MissingTable:
+ def __init__(self, table):
+ self._table = table
+ def get(self, codon, stop_symbol):
+ try:
+ return self._table.get(codon, stop_symbol)
+ except CodonTable.TranslationError:
+ return 'X'
+
+def makeTableX(table):
+ assert table.protein_alphabet == IUPAC.extended_protein
+ return CodonTable.CodonTable(table.nucleotide_alphabet, proteinX,
+ MissingTable(table.forward_table),
+ table.back_table, table.start_codons,
+ table.stop_codons)
+
+# end of hacks
+
+def seq3(seq):
+ """Turn a one letter code protein sequence into one with three letter codes.
+
+ The single input argument 'seq' should be a protein sequence using single
+ letter codes, either as a python string or as a Seq or MutableSeq object.
+
+ This function returns the amino acid sequence as a string using the three
+ letter amino acid codes. Output follows the IUPAC standard (including
+ ambiguous characters B for "Asx", J for "Xle" and X for "Xaa", and also U
+ for "Sel" and O for "Pyl") plus "Ter" for a terminator given as an asterisk. Any unknown
+ character (including possible gap characters), is changed into 'Xaa'.
+
+ e.g.
+ >>> from Bio.SeqUtils import seq3
+ >>> seq3("MAIVMGRWKGAR*")
+ 'MetAlaIleValMetGlyArgTrpLysGlyAlaArgTer'
+
+ This function was inspired by BioPerl's seq3.
+ """
+ threecode = {'A':'Ala', 'B':'Asx', 'C':'Cys', 'D':'Asp',
+ 'E':'Glu', 'F':'Phe', 'G':'Gly', 'H':'His',
+ 'I':'Ile', 'K':'Lys', 'L':'Leu', 'M':'Met',
+ 'N':'Asn', 'P':'Pro', 'Q':'Gln', 'R':'Arg',
+ 'S':'Ser', 'T':'Thr', 'V':'Val', 'W':'Trp',
+ 'Y':'Tyr', 'Z':'Glx', 'X':'Xaa', '*':'Ter',
+ 'U':'Sel', 'O':'Pyl', 'J':'Xle',
+ }
+ #We use a default of 'Xaa' for undefined letters
+ #Note this will map '-' to 'Xaa' which may be undesirable!
+ return ''.join([threecode.get(aa,'Xaa') for aa in seq])
+
+
+# }}}
+
+######################################
+# Mixed ???
+######################
+# {{{
+
+def translate(seq, frame = 1, genetic_code = 1, translator = None):
+ """Translation of DNA in one of the six different reading frames (DEPRECATED).
+
+ Use the Bio.Seq.Translate function, or the Seq object's translate method
+ instead:
+
+ >>> from Bio.Seq import Seq
+ >>> my_seq = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG")
+ >>> my_seq = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUA")
+ >>> for frame in [0,1,2] :
+ ... print my_seq[frame:].translate()
+ ...
+ MAIVMGR*KGAR*
+ WPL*WAAERVPDS
+ GHCNGPLKGCPIV
+ >>> for frame in [0,1,2] :
+ ... print my_seq.reverse_complement()[frame:].translate()
+ ...
+ YYRAPFQRPITMA
+ TIGHPFSGPLQWP
+ LSGTLSAAHYNGH
+ """
+ import warnings
+ warnings.warn("Bio.SeqUtils.translate() has been deprecated, and we intend" \
+ +" to remove it in a future release of Biopython. Please use"\
+ +" the method or function in Bio.Seq instead, as described in"\
+ +" the Tutorial.", DeprecationWarning)
+
+ if frame not in [1,2,3,-1,-2,-3]:
+ raise ValueError('invalid frame')
+
+ if not translator:
+ table = makeTableX(CodonTable.ambiguous_dna_by_id[genetic_code])
+ translator = Translate.Translator(table)
+
+ #Does this frame calculation do something sensible? No RC taken!
+ return translator.translate(Seq(seq[frame-1:], IUPAC.ambiguous_dna)).data
+
+def GC_Frame(seq, genetic_code = 1):
+ """Just an alias for six_frame_translations (OBSOLETE).
+
+ Use six_frame_translation directly, as this function may be deprecated
+ in a future release."""
+ return six_frame_translations(seq, genetic_code)
+
+def six_frame_translations(seq, genetic_code = 1):
+ """Formatted string showing the 6 frame translations and GC content.
+
+ nice looking 6 frame translation with GC content - code from xbbtools
+ similar to DNA Striders six-frame translation
+
+ e.g.
+ from Bio.SeqUtils import six_frame_translations
+ print six_frame_translations("AUGGCCAUUGUAAUGGGCCGCUGA")
+ """
+ from Bio.Seq import reverse_complement, translate
+ anti = reverse_complement(seq)
+ comp = anti[::-1]
+ length = len(seq)
+ frames = {}
+ for i in range(0,3):
+ frames[i+1] = translate(seq[i:], genetic_code)
+ frames[-(i+1)] = reverse(translate(anti[i:], genetic_code))
+
+ # create header
+ if length > 20:
+ short = '%s ... %s' % (seq[:10], seq[-10:])
+ else:
+ short = seq
+ #TODO? Remove the date as this would spoil any unit test...
+ date = time.strftime('%y %b %d, %X', time.localtime(time.time()))
+ header = 'GC_Frame: %s, ' % date
+ for nt in ['a','t','g','c']:
+ header += '%s:%d ' % (nt, seq.count(nt.upper()))
+
+ header += '\nSequence: %s, %d nt, %0.2f %%GC\n\n\n' % (short.lower(),length, GC(seq))
+ res = header
+
+ for i in range(0,length,60):
+ subseq = seq[i:i+60]
+ csubseq = comp[i:i+60]
+ p = i/3
+ res = res + '%d/%d\n' % (i+1, i/3+1)
+ res = res + ' ' + ' '.join(map(None,frames[3][p:p+20])) + '\n'
+ res = res + ' ' + ' '.join(map(None,frames[2][p:p+20])) + '\n'
+ res = res + ' '.join(map(None,frames[1][p:p+20])) + '\n'
+ # seq
+ res = res + subseq.lower() + '%5d %%\n' % int(GC(subseq))
+ res = res + csubseq.lower() + '\n'
+ # - frames
+ res = res + ' '.join(map(None,frames[-2][p:p+20])) +' \n'
+ res = res + ' ' + ' '.join(map(None,frames[-1][p:p+20])) + '\n'
+ res = res + ' ' + ' '.join(map(None,frames[-3][p:p+20])) + '\n\n'
+ return res
+
+# }}}
+
+######################################
+# FASTA file utilities
+######################
+# {{{
+
+def fasta_uniqids(file):
+ """Checks and changes the name/ID's to be unique identifiers by adding numbers (OBSOLETE).
+
+ file - a FASTA format filename to read in.
+
+ No return value, the output is written to screen.
+ """
+ dict = {}
+ txt = open(file).read()
+ entries = []
+ for entry in txt.split('>')[1:]:
+ name, seq= entry.split('\n',1)
+ name = name.split()[0].split(',')[0]
+
+ if name in dict:
+ n = 1
+ while 1:
+ n = n + 1
+ _name = name + str(n)
+ if _name not in dict:
+ name = _name
+ break
+
+ dict[name] = seq
+
+ for name, seq in dict.items():
+ print '>%s\n%s' % (name, seq)
+
+def quick_FASTA_reader(file):
+ """Simple FASTA reader, returning a list of string tuples.
+
+ The single argument 'file' should be the filename of a FASTA format file.
+ This function will open and read in the entire file, constructing a list
+ of all the records, each held as a tuple of strings (the sequence name or
+ title, and its sequence).
+
+ This function was originally intended for use on large files, where its
+ low overhead makes it very fast. However, because it returns the data as
+ a single in memory list, this can require a lot of RAM on large files.
+
+ You are generally encouraged to use Bio.SeqIO.parse(handle, "fasta") which
+ allows you to iterate over the records one by one (avoiding having all the
+ records in memory at once). Using Bio.SeqIO also makes it easy to switch
+ between different input file formats. However, please note that rather
+ than simple strings, Bio.SeqIO uses SeqRecord objects for each record.
+ """
+ #Want to split on "\n>" not just ">" in case there are any extra ">"
+ #in the name/description. So, in order to make sure we also split on
+ #the first entry, prepend a "\n" to the start of the file.
+ handle = open(file)
+ txt = "\n" + handle.read()
+ handle.close()
+ entries = []
+ for entry in txt.split('\n>')[1:]:
+ name,seq= entry.split('\n',1)
+ seq = seq.replace('\n','').replace(' ','').upper()
+ entries.append((name, seq))
+ return entries
+
+def apply_on_multi_fasta(file, function, *args):
+ """Apply a function on each sequence in a multiple FASTA file (OBSOLETE).
+
+ file - filename of a FASTA format file
+ function - the function you wish to invoke on each record
+ *args - any extra arguments you want passed to the function
+
+ This function will iterate over each record in a FASTA file as SeqRecord
+ objects, calling your function with the record (and supplied args) as
+ arguments.
+
+ This function returns a list. For those records where your function
+ returns a value, this is taken as a sequence and used to construct a
+ FASTA format string. If your function never has a return value, this
+ means apply_on_multi_fasta will return an empty list.
+ """
+ try:
+ f = globals()[function]
+ except:
+ raise NotImplementedError("%s not implemented" % function)
+
+ handle = open(file, 'r')
+ records = SeqIO.parse(handle, "fasta")
+ results = []
+ for record in records:
+ arguments = [record.sequence]
+ for arg in args: arguments.append(arg)
+ result = f(*arguments)
+ if result:
+ results.append('>%s\n%s' % (record.name, result))
+ handle.close()
+ return results
+
+def quicker_apply_on_multi_fasta(file, function, *args):
+ """Apply a function on each sequence in a multiple FASTA file (OBSOLETE).
+
+ file - filename of a FASTA format file
+ function - the function you wish to invoke on each record
+ *args - any extra arguments you want passed to the function
+
+ This function will use quick_FASTA_reader to load every record in the
+ FASTA file into memory as a list of tuples. For each record, it will
+ call your supplied function with the record as a tuple of the name and
+ sequence as strings (plus any supplied args).
+
+ This function returns a list. For those records where your function
+ returns a value, this is taken as a sequence and used to construct a
+ FASTA format string. If your function never has a return value, this
+ means quicker_apply_on_multi_fasta will return an empty list.
+ """
+ try:
+ f = globals()[function]
+ except:
+ raise NotImplementedError("%s not implemented" % function)
+
+ entries = quick_FASTA_reader(file)
+ results = []
+ for name, seq in entries:
+ arguments = [seq]
+ for arg in args: arguments.append(arg)
+ result = f(*arguments)
+ if result:
+ results.append('>%s\n%s' % (name, result))
+ handle.close()
+ return results
+
+# }}}
+
+######################################
+# Main
+#####################
+# {{{
+
+if __name__ == '__main__':
+ import sys, getopt
+ # crude command line options to use most functions directly on a FASTA file
+ options = {'apply_on_multi_fasta':0,
+ 'quick':0,
+ 'uniq_ids':0,
+ }
+
+ optlist, args = getopt.getopt(sys.argv[1:], '', ['describe', 'apply_on_multi_fasta=',
+ 'help', 'quick', 'uniq_ids', 'search='])
+ for arg in optlist:
+ if arg[0] in ['-h', '--help']:
+ pass
+ elif arg[0] in ['--describe']:
+ # get all new functions from this file
+ mol_funcs = [x[0] for x in locals().items() if type(x[1]) == type(GC)]
+ mol_funcs.sort()
+ print 'available functions:'
+ for f in mol_funcs: print '\t--%s' % f
+ print '\n\ne.g.\n./sequtils.py --apply_on_multi_fasta GC test.fas'
+
+ sys.exit(0)
+ elif arg[0] in ['--apply_on_multi_fasta']:
+ options['apply_on_multi_fasta'] = arg[1]
+ elif arg[0] in ['--search']:
+ options['search'] = arg[1]
+ else:
+ key = re.search('-*(.+)', arg[0]).group(1)
+ options[key] = 1
+
+
+ if options.get('apply_on_multi_fasta'):
+ file = args[0]
+ function = options['apply_on_multi_fasta']
+ arguments = []
+ if options.get('search'):
+ arguments = options['search']
+ if function == 'xGC_skew':
+ arguments = 1000
+ if options.get('quick'):
+ results = quicker_apply_on_multi_fasta(file, function, arguments)
+ else:
+ results = apply_on_multi_fasta(file, function, arguments)
+ for result in results: print result
+
+ elif options.get('uniq_ids'):
+ file = args[0]
+ fasta_uniqids(file)
+
+# }}}
+
--- /dev/null
+# Copyright 2003, 2007 by Sebastian Bassi. sbassi@genesdigitales.com
+# All rights reserved. This code is part of the Biopython
+# distribution and governed by its license.
+# Please see the LICENSE file that should have been included as part
+# of this package.
+
+import math
+
+def lcc_mult(seq,wsize):
+ """Local Composition Complexity (LCC) values over sliding window.
+
+ Returns a list of floats, the LCC values for a sliding window over
+ the sequence.
+
+ seq - an unambiguous DNA sequence (a string or Seq object)
+ wsize - window size, integer
+
+ The result is the same as applying lcc_simp multiple times, but this
+ version is optimized for speed. The optimization works by using the
+ value of previous window as a base to compute the next one."""
+ l2=math.log(2)
+ tamseq=len(seq)
+ try :
+ #Assume its a string
+ upper = seq.upper()
+ except AttributeError :
+ #Should be a Seq object then
+ upper = seq.tostring().upper()
+ compone=[0]
+ lccsal=[0]
+ for i in range(wsize):
+ compone.append(((i+1)/float(wsize))*
+ ((math.log((i+1)/float(wsize)))/l2))
+ window=seq[0:wsize]
+ cant_a=window.count('A')
+ cant_c=window.count('C')
+ cant_t=window.count('T')
+ cant_g=window.count('G')
+ term_a=compone[cant_a]
+ term_c=compone[cant_c]
+ term_t=compone[cant_t]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ tail=seq[0]
+ for x in range (tamseq-wsize):
+ window=upper[x+1:wsize+x+1]
+ if tail==window[-1]:
+ lccsal.append(lccsal[-1])
+ elif tail=='A':
+ cant_a=cant_a-1
+ if window.endswith('C'):
+ cant_c=cant_c+1
+ term_a=compone[cant_a]
+ term_c=compone[cant_c]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('T'):
+ cant_t=cant_t+1
+ term_a=compone[cant_a]
+ term_t=compone[cant_t]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('G'):
+ cant_g=cant_g+1
+ term_a=compone[cant_a]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif tail=='C':
+ cant_c=cant_c-1
+ if window.endswith('A'):
+ cant_a=cant_a+1
+ term_a=compone[cant_a]
+ term_c=compone[cant_c]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('T'):
+ cant_t=cant_t+1
+ term_c=compone[cant_c]
+ term_t=compone[cant_t]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('G'):
+ cant_g=cant_g+1
+ term_c=compone[cant_c]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif tail=='T':
+ cant_t=cant_t-1
+ if window.endswith('A'):
+ cant_a=cant_a+1
+ term_a=compone[cant_a]
+ term_t=compone[cant_t]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('C'):
+ cant_c=cant_c+1
+ term_c=compone[cant_c]
+ term_t=compone[cant_t]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('G'):
+ cant_g=cant_g+1
+ term_t=compone[cant_t]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif tail=='G':
+ cant_g=cant_g-1
+ if window.endswith('A'):
+ cant_a=cant_a+1
+ term_a=compone[cant_a]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('C'):
+ cant_c=cant_c+1
+ term_c=compone[cant_c]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ elif window.endswith('T'):
+ cant_t=cant_t+1
+ term_t=compone[cant_t]
+ term_g=compone[cant_g]
+ lccsal.append(-(term_a+term_c+term_t+term_g))
+ tail=window[0]
+ return lccsal
+
+def lcc_simp(seq):
+ """Local Composition Complexity (LCC) for a sequence.
+
+ seq - an unambiguous DNA sequence (a string or Seq object)
+
+ Returns the Local Composition Complexity (LCC) value for the entire
+ sequence (as a float).
+
+ Reference:
+ Andrzej K Konopka (2005) Sequence Complexity and Composition
+ DOI: 10.1038/npg.els.0005260
+ """
+ wsize=len(seq)
+ try :
+ #Assume its a string
+ upper = seq.upper()
+ except AttributeError :
+ #Should be a Seq object then
+ upper = seq.tostring().upper()
+ l2=math.log(2)
+ if 'A' not in seq:
+ term_a=0
+ # Check to avoid calculating the log of 0.
+ else:
+ term_a=((upper.count('A'))/float(wsize))*((math.log((upper.count('A'))
+ /float(wsize)))/l2)
+ if 'C' not in seq:
+ term_c=0
+ else:
+ term_c=((upper.count('C'))/float(wsize))*((math.log((upper.count('C'))
+ /float(wsize)))/l2)
+ if 'T' not in seq:
+ term_t=0
+ else:
+ term_t=((upper.count('T'))/float(wsize))*((math.log((upper.count('T'))
+ /float(wsize)))/l2)
+ if 'G' not in seq:
+ term_g=0
+ else:
+ term_g=((upper.count('G'))/float(wsize))*((math.log((upper.count('G'))
+ /float(wsize)))/l2)
+ lccsal=-(term_a+term_c+term_t+term_g)
+ return lccsal
--- /dev/null
+# This is a Python module.
+"""This module is DEPRECATED.
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+and associate ones like Bio.Std are now deprecated. They are no longer
+used in any of the current Biopython parsers, and are likely to be removed
+in a future release.
+"""
+
+import warnings
+warnings.warn("Martel and those parts of Biopython depending on it" \
+ +" directly (such as Bio.Mindy and Bio.Std) are now" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+# Standard Bioformats definitions
+
+import Martel
+Group = Martel.Group
+
+namespace = "bioformat"
+NS = namespace + ":"
+XMLNS = "http://biopython.org/bioformat"
+
+def _set_if_given(attrs, field, d, valid = None, convert = None):
+ value = attrs.get(field)
+ if value is not None:
+ if valid is not None:
+ if value not in valid:
+ raise TypeError("%s (%r) must be one of %s" % \
+ (field, value, valid))
+ if convert is None:
+ d[field] = value
+ else:
+ d[field] = convert(value)
+
+def _complain_if_given(attrs, name):
+ if attrs.has_key(name) and attrs[name] is not None:
+ raise NotImplementedError("Don't yet handle %r" % (name,))
+
+def _must_have(expr, f):
+ tag = f.tag
+ if tag not in expr.group_names():
+ raise TypeError(
+ "group %r not present in the expression but is required" % \
+ (tag,))
+
+def _must_have_set(expr, sets):
+ names = expr.group_names()
+ for set in sets:
+ for f in set:
+ tag = f.tag
+ if tag not in names:
+ break
+ else:
+ return
+ if len(sets) == 1:
+ raise TypeError("missing required tags (need %s) in expression" %
+ [f.tag for f in sets[0]])
+ lines = ["missing required tags in expression; must have one set from:"]
+ for set in sets:
+ lines.append( str( [t.tag for f in set] ) )
+ s = "\n".join(lines)
+ raise TypeError(s)
+
+def _must_not_have(expr, f):
+ f.tag
+ if tag in expr.group_names():
+ raise TypeError(
+ "group %r present in the expression but is not allowed" % \
+ (tag,))
+
+
+# pre- Python 2.2 functions didn't allow attributes
+def _f():
+ pass
+try:
+ _f.x = 1
+ _use_hack = 0
+except AttributeError:
+ _use_hack = 1
+del _f
+
+def _check_name(f, text):
+ if text == "record": # XXX FIXME
+ return
+ assert NS + f.func_name == text, (NS + ":" + f.func_name, text)
+
+def _check_attrs(attrs, names):
+ for name in attrs.keys():
+ if name not in names:
+ raise TypeError("attr %r is not allowed here (valid terms: %s)" % \
+ (name, names))
+ d = attrs.copy()
+ for name in names:
+ if not d.has_key(name):
+ d[name] = None
+ return d
+
+if not _use_hack:
+ def _settag(f, tag):
+ _check_name(f, tag)
+ f.tag = tag
+else:
+ # Convert the functions into callable objects
+ class StdTerm:
+ def __init__(self, func):
+ self._func = func
+ def __call__(self, *args, **kwargs):
+ return self._func( *args, **kwargs)
+
+ def _settag(f, tag):
+ _check_name(f, tag)
+ x = globals()[f.func_name] = StdTerm(f)
+ x.tag = tag
+
+################ identifier, description, and cross-references
+def record(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("format",))
+ d = {"xmlns:bioformat": XMLNS}
+ _set_if_given(attrs, "format", d)
+ return Group("record", expr, d) # XXX FIXME
+_settag(record, "record") # XXX AND FIXME
+
+
+def dbid(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("type", "style", "dbname"))
+ d = {}
+ _set_if_given(attrs, "type", d, ("primary", "accession", "secondary"))
+ _set_if_given(attrs, "dbname", d)
+ return Group(NS + "dbid", expr, d)
+_settag(dbid, NS + "dbid")
+
+def description_block(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("join",))
+ _must_have(expr, description)
+ d = {}
+ _set_if_given(attrs, "join", d, ("english", "concat", "space", "newline"))
+ return Group(NS + "description_block", expr, d)
+_settag(description_block, NS + "description_block")
+
+def description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "description", expr)
+_settag(description, NS + "description")
+
+def description_line(expr, attrs = {}):
+ return description_block(description(expr, attrs))
+
+def fast_dbxref(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("style",))
+ d = {}
+ _set_if_given(attrs, "style", d, ("sp-general", "sp-prosite", "sp-embl"))
+ return Group(NS + "fast_dbxref", expr, d)
+
+def dbxref(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("style",))
+ _must_have(expr, dbxref_dbid)
+ d = {}
+ _complain_if_given(attrs, "style")
+ return Group(NS + "dbxref", expr, d)
+_settag(dbxref, NS + "dbxref")
+
+def dbxref_dbname(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("style",))
+ d = {}
+ _set_if_given(attrs, "style", d)
+ return Group(NS + "dbxref_dbname", expr, d)
+_settag(dbxref_dbname, NS + "dbxref_dbname")
+
+def dbxref_dbid(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("dbname", "type", "style", "negate"))
+ d = {}
+ _set_if_given(attrs, "dbname", d)
+ _set_if_given(attrs, "type", d, ("primary", "accession", "secondary"))
+ _complain_if_given(attrs, "style")
+ _set_if_given(attrs, "negate", d, (0, 1), str)
+
+ return Group(NS + "dbxref_dbid", expr, d)
+_settag(dbxref_dbid, NS + "dbxref_dbid")
+
+def dbxref_negate(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "dbxref_negate", expr)
+_settag(dbxref_negate, NS + "dbxref_negate")
+
+##################### sequences
+
+def _check_gapchar(s):
+ if not ( ord(" ") <= ord(s) <= 126 ):
+ raise TypeError("%r not allowed as a gap character" % (s,))
+ return s
+
+# What about three letter codes?
+def sequence_block(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("alphabet", "gapchar", "remove_spaces"))
+ _must_have(expr, sequence)
+ d = {}
+ _set_if_given(attrs, "alphabet", d,
+ ("iupac-protein", "iupac-dna", "iupac-rna",
+ "iupac-ambiguous-protein",
+ "iupac-ambiguous-dna",
+ "iupac-ambiguous-rna",
+ "protein", "dna", "rna", "unknown"))
+ _set_if_given(attrs, "gapchar", d, convert = _check_gapchar)
+ _set_if_given(attrs, "remove_spaces", d, (0, 1), str)
+ return Group(NS + "sequence_block", expr, d)
+_settag(sequence_block, NS + "sequence_block")
+
+def sequence(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "sequence", expr)
+_settag(sequence, NS + "sequence")
+
+def alphabet(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("alphabet",))
+ d = {}
+ _set_if_given(attrs, "alphabet", d,
+ ("iupac-protein", "iupac-dna", "iupac-rna",
+ "iupac-ambiguous-protein",
+ "iupac-ambiguous-dna",
+ "iupac-ambiguous-rna",
+ "protein", "dna", "rna", "nucleotide", "unknown"))
+ return Group(NS + "alphabet", expr, d)
+_settag(alphabet, NS + "alphabet")
+
+
+
+############################## features
+
+# In PIR
+
+# FEATURE
+# 1-25 #domain signal sequence #status predicted #label SIG\
+# 26-737 #product procollagen-lysine 5-dioxygenase 2 #status
+# predicted #label MAT\
+# 63,209,297,365,522,
+# 725 #binding_site carbohydrate (Asn) (covalent) #status
+# predicted
+
+# The whole thing is a 'feature_block'
+
+# One 'feature' is
+# 26-737 #product procollagen-lysine 5-dioxygenase 2 #status
+# predicted #label MAT\
+
+# One 'feature_name' is "binding_site".
+
+# An example of the feature_location_block and feature_block, which I
+# will abbreviate as 'flb' and 'fl', is:
+# <flb> <fl>63,209,297,365,522,</fl>
+# <fl>725</fl> #binding_site carbohydrate ...
+
+# PIR doesn't have a 'feature_description'
+
+# Let:
+# fq = feature_qualifier
+# fqb = feature_qualifier
+# fqn = feature_qualifier_name
+# fqd = feature_qualifier_description
+# then the text
+#
+# 26-737 #product procollagen-lysine 5-dioxygenase 2 #status
+# predicted #label MAT\
+#
+# can be represented as (the rather tedious)
+#
+# 26-737 <fqb><fq>#<fqn>product</fqn> <fqd>procollagen-\
+# lysine 5-dioxygenase 2</fqd></fq> #<fq><fqn>status</fqn>
+# <fqd>predicted</fqd> #<fq><fqn>label\
+# </fqn> <fqd>MAT</fqd></fq>\</fqb>
+#
+
+# 'style' determines the namespace for the feature name
+def feature_block(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("style", "location-style"))
+ d = {}
+ _set_if_given(attrs, "style", d)
+ _set_if_given(attrs, "location-style", d)
+ _must_have(expr, feature)
+ return Group(NS + "feature_block", expr, d)
+_settag(feature_block, NS + "feature_block")
+
+def feature(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("location-style",))
+ d = {}
+ _set_if_given(attrs, "location-style", d)
+ _must_have(expr, feature_name)
+ _must_have_set(expr, [[feature_location],
+ [feature_location_start, feature_location_end]])
+ return Group(NS + "feature", expr, d)
+_settag(feature, NS + "feature")
+
+def feature_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_name", expr)
+_settag(feature_name, NS + "feature_name")
+
+def feature_location(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_location", expr)
+_settag(feature_location, NS + "feature_location")
+
+def feature_location_start(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_location_start", expr)
+_settag(feature_location_start, NS + "feature_location_start")
+
+def feature_location_end(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_location_end", expr)
+_settag(feature_location_end, NS + "feature_location_end")
+
+def feature_description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_description", expr)
+_settag(feature_description, NS + "feature_description")
+
+
+##def feature_qualifier_block(expr, attrs = {}):
+## attrs = _check_attrs(attrs, ())
+## _must_have(expr, feature_qualifier)
+## return Group(NS + "feature_qualifier_block", expr)
+##_settag(feature_qualifier_block, NS + "feature_qualifier_block")
+
+def feature_qualifier(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ _must_have(expr, feature_qualifier_name)
+ return Group(NS + "feature_qualifier", expr)
+_settag(feature_qualifier, NS + "feature_qualifier")
+
+def feature_qualifier_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_qualifier_name", expr)
+_settag(feature_qualifier_name, NS + "feature_qualifier_name")
+
+def feature_qualifier_description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group(NS + "feature_qualifier_description", expr)
+_settag(feature_qualifier_description, NS + "feature_qualifier_description")
+
+
+############ For homology searches
+
+# "BLASTN", "BLASTP"
+def application_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("app",))
+ return Group("bioformat:application_name", expr, attrs)
+
+# "2.0.11", "2.0a19MP-WashU"
+def application_version(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:application_version", expr, attrs)
+
+def search_header(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:search_header", expr, attrs)
+
+def search_table(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:search_table", expr, attrs)
+
+def search_table_description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("bioformat:decode",))
+ d = {"bioformat:decode": "strip"}
+ _set_if_given(attrs, "bioformat:decode", d)
+ return Group("bioformat:search_table_description", expr, d)
+
+def search_table_value(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("name", "bioformat:decode"))
+ return Group("bioformat:search_table_value", expr, attrs)
+
+def search_table_entry(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:search_table_entry", expr, attrs)
+
+def query_description_block(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("join-query",))
+ d = {"join-query": "join|fixspaces"}
+ _set_if_given(attrs, "join-query", d)
+ return Group("bioformat:query_description_block", expr, d)
+
+def query_description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("bioformat:decode"))
+ d = {}
+ _set_if_given(attrs, "bioformat:decode", d)
+ return Group("bioformat:query_description", expr, d)
+
+def query_size(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:query_size", expr)
+
+def database_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:database_name", expr, attrs)
+
+def database_num_sequences(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("bioformat:decode",))
+ return Group("bioformat:database_num_sequences", expr, attrs)
+
+def database_num_letters(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("bioformat:decode",))
+ return Group("bioformat:database_num_letters", expr, attrs)
+
+def hit(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("join-description",))
+ d = {"join-description": "join|fixspaces"}
+ _set_if_given(attrs, "join-description", d)
+ return Group("bioformat:hit", expr, d)
+
+def hit_length(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hit_length", expr, attrs)
+
+def hit_description(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("bioformat:decode"))
+ d = {}
+ _set_if_given(attrs, "bioformat:decode", d)
+ return Group("bioformat:hit_description", expr, d)
+
+def hsp(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp", expr, attrs)
+
+def hsp_value(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("name", "bioformat:decode"))
+ return Group("bioformat:hsp_value", expr, attrs)
+
+def hsp_frame(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("which",))
+ d = {}
+ _set_if_given(attrs, "which", d, valid = ("query", "homology", "subject"))
+ return Group("bioformat:hsp_frame", expr, d)
+
+def hsp_strand(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("strand", "which"))
+ d = {}
+ _set_if_given(attrs, "which", d, valid = ("query", "homology", "subject"))
+ _set_if_given(attrs, "strand", d, valid = ("+1", "0", "-1", ""))
+ return Group("bioformat:hsp_strand", expr, d)
+
+def hsp_seqalign_query_seq(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_query_seq", expr, attrs)
+
+def hsp_seqalign_homology_seq(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_homology_seq", expr, attrs)
+
+def hsp_seqalign_subject_seq(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_subject_seq", expr, attrs)
+
+def hsp_seqalign_query_leader(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_query_leader", expr, attrs)
+
+
+def hsp_seqalign_query_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_query_name", expr, attrs)
+
+def hsp_seqalign_subject_name(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_subject_name", expr, attrs)
+
+def hsp_seqalign(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign", expr, attrs)
+
+def hsp_seqalign_query_start(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_query_start", expr, attrs)
+
+def hsp_seqalign_query_end(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_query_end", expr, attrs)
+
+def hsp_seqalign_subject_start(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_subject_start", expr, attrs)
+
+def hsp_seqalign_subject_end(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ())
+ return Group("bioformat:hsp_seqalign_subject_end", expr, attrs)
+
+def search_parameter(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("name", "bioformat:decode"))
+ d = {}
+ _set_if_given(attrs, "name", d)
+ _set_if_given(attrs, "bioformat:decode", d)
+ return Group("bioformat:search_parameter", expr, d)
+
+def search_statistic(expr, attrs = {}):
+ attrs = _check_attrs(attrs, ("name", "bioformat:decode"))
+ d = {}
+ _set_if_given(attrs, "name", d)
+ _set_if_given(attrs, "bioformat:decode", d)
+ return Group("bioformat:search_statistic", expr, d)
+
--- /dev/null
+# Standard Content and Dispatch handlers for the Bioformat IO system
+# This is a Python module.
+"""This module is DEPRECATED.
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+and associate ones like Bio.StdHandler are now deprecated. They are no longer
+used in any of the current Biopython parsers, and are likely to be removed
+in a future release.
+"""
+
+import warnings
+warnings.warn("Martel and those parts of Biopython depending on it" \
+ +" directly (such as Bio.Mindy and Bio.StdHandler) are now" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+
+from xml.sax import handler
+from Martel import Parser, Dispatch
+from Bio import Std, Decode
+
+###################################
+
+# Helper functions to make functions
+
+def add_int_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s = int(self.get_characters())
+""" % attrname
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s = self.get_characters()
+""" % attrname
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_dict_handler(klass, tag, attrname, key):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s["%s"] = self.get_characters()
+""" % (attrname, key)
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_decode_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ self._decode_%s = attrs.get("bioformat:decode", None)
+ def end(self, tag):
+ if self._decode_%s is not None:
+ s = Decode.make_decoder(self._decode_%s)(s)
+ self.%s = self.get_characters()
+""" % (tag, tag, tag, attrname)
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_first_text_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ if self.%s is None:
+ self.save_characters()
+ def end(self, tag):
+ if self.%s is None:
+ self.%s = self.get_characters()
+""" % (attrname, attrname, attrname)
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_block_handler(klass, tag, joinattr, defaultjoin, attrname):
+ assert not hasattr(klass, "start_" + tag), "existing method exists"
+ assert not hasattr(klass, "end_" + tag), "existing method exists"
+ assert not hasattr(klass, "start_"+tag+"_block"), "existing method exists"
+ assert not hasattr(klass, "end_" +tag+"_block"), "existing method exists"
+ s = """if 1:
+ def start_block(self, tag, attrs):
+ self._%(tag)s_join_func = Decode.make_decoder(attrs.get(%(joinattr)r, %(defaultjoin)r))
+ self._%(tag)s_lines = []
+ def end_block(self, tag):
+ self.%(attrname)s = self._%(tag)s_join_func(self._%(tag)s_lines)
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self._%(tag)s_lines.append(self.get_characters())
+""" % locals()
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+ setattr(klass, "start_" + tag + "_block", d["start_block"])
+ setattr(klass, "end_" + tag + "_block", d["end_block"])
+
+def add_value_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self._%(tag)s_name = attrs["name"]
+ self._%(tag)s_decode = attrs.get("bioformat:decode", None)
+ self.save_characters()
+ def end(self, tag):
+ s = self.get_characters()
+ if self._%(tag)s_decode is not None:
+ s = Decode.make_decoder(self._%(tag)s_decode)(s)
+ self.%(attrname)s[self._%(tag)s_name] = s
+""" % locals()
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+
+#################################
+
+class ConvertHandler(handler.ContentHandler):
+ """Used to read records and produce output"""
+ def __init__(self, record_builder, writer, record_tag = "record"):
+ handler.ContentHandler.__init__(self)
+ self.record_builder = record_builder
+ self.writer = writer
+ self.record_tag = record_tag
+
+ def startDocument(self):
+ self.inside_record = 0
+ self.characters = self.ignore_characters
+
+ def startElement(self, tag, attrs):
+ if self.inside_record:
+ self.record_builder.startElement(tag, attrs)
+ elif tag == self.record_tag:
+ self.record_builder.startDocument()
+ self.inside_record = 1
+ self.characters = self.record_builder.characters
+ self.record_builder.startElement(tag, attrs)
+
+ def endElement(self, tag):
+ if self.inside_record:
+ self.record_builder.endElement(tag)
+ if tag == self.record_tag:
+ self.record_builder.endDocument()
+ self.writer.write(self.record_builder.document)
+ self.inside_record = 0
+ self.characters = self.ignore_characters
+
+ def ignore_characters(self, s):
+ pass
+
+class ConvertDispatchHandler(Dispatch.Dispatcher):
+ """Used to read records and produce output through a Dispatcher"""
+ def __init__(self, record_builder, writer, record_tag = "record"):
+ setattr(self, "end_" + record_tag, self.write_record)
+ Dispatch.Dispatcher.__init__(self,
+ remap = {record_tag: "bioformat:"}
+ )
+ self.acquire(record_builder)
+ self.record_builder = record_builder
+ self.writer = writer
+ self.record_tag = record_tag
+ def write_record(self, tag):
+ self.writer.write(self.record_builder.document)
+
+
+
+class RecognizeHandler(handler.ContentHandler, handler.ErrorHandler):
+ def __init__(self):
+ self.recognized = 1
+ self.exc = None
+
+ def fatalError(self, exc):
+ if isinstance(exc, Parser.ParserIncompleteException):
+ pass
+ else:
+ self.recognized = 0
+ self.exc = exc
+ raise exc
+
+ error = fatalError
+
+ def endElement(self, tag):
+ if tag == "record":
+ raise Parser.ParserException("we finished a record!")
+
+
+
+class Handle_dbid(Dispatch.Callback):
+ def start_dbid(self, tag, attrs):
+ self.attrs = attrs
+ self.save_characters()
+
+ def end_dbid(self, tag):
+ text = self.get_characters()
+ self.callback(text, self.attrs)
+
+
+class Handle_description(Dispatch.Callback):
+ def start_description_block(self, tag, attrs):
+ j = attrs.get("join", None)
+ if j is None:
+ self.join_fctn = Decode.join_fixspaces
+ else:
+ self.join_fctn = Decode.make_typechecked_decoder(j, list, str)
+ self.descriptions = []
+ def start_description(self, tag, attrs):
+ self.save_characters()
+ def end_description(self, tag):
+ x = self.get_characters()
+ self.descriptions.append(x)
+ def end_description_block(self, tag):
+ self.callback(self.join_fctn(self.descriptions))
+
+#### There can be multiple dbxref_dbids in a dbxref
+# DR EMBL; X64411; CAA45756.1; -.
+# <dbxref><..dbname style="swiss">EMBL</..dbname>
+# <dbid type="primary">X64411</dbid>
+# <dbid type="accession">CAA45756.1</dbid>
+# </dbxref>
+###
+# DR P35156, YPUI_BACSU, F;
+# <dbxref><dbid type="primary" dbname="sprot">P35156</dbid>
+# <dbid type="accession" dbname="sprot">YPUI_BACSU</dbid>
+# <negate/>
+# </dbxref>
+
+def _fixup_sp_pattern(exp):
+ import re
+ import Martel
+ exp = Martel.select_names(exp, (Std.dbxref_dbname.tag,Std.dbxref_dbid.tag))
+
+ e = exp._find_groups(Std.dbxref_dbname.tag)
+ assert len(e) == 1
+ e = e[0]
+ e.name = "dbname"
+ dbstyle = e.attrs["style"]
+ e.attrs = {}
+ e = exp._find_groups(Std.dbxref_dbid.tag)
+ assert len(e) == 2
+ e[0].name = "primary_dbid"
+ primary_type = e[0].attrs["type"]
+ e[0].attrs = {}
+ e[1].name = "secondary_dbid"
+ secondary_type = e[1].attrs["type"]
+ e[1].attrs = {}
+ pattern = str(exp) + "$"
+ pat = re.compile(pattern)
+ return pat, dbstyle, primary_type, secondary_type
+
+# Turns out these 'fast' versions speed up the dbxref code by about
+# a factor of 2.
+
+# DR PIR; S08427; S08427.
+_fast_dbxref_sp_general_data = None
+def _fast_dbxref_sp_general(s):
+ global _fast_dbxref_sp_general_data
+ if _fast_dbxref_sp_general_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_general_data = _fixup_sp_pattern(
+ sprot38.real_DR_general)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_general_data
+
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-general dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+# DR PFAM; PF01018; GTP1_OBG; 1.
+# DR PROSITE; PS00905; GTP1_OBG; 1.
+
+_fast_dbxref_sp_prosite_data = None
+def _fast_dbxref_sp_prosite(s):
+ global _fast_dbxref_sp_prosite_data
+
+ if _fast_dbxref_sp_prosite_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_prosite_data = _fixup_sp_pattern(
+ sprot38.real_DR_prosite)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_prosite_data
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-prosite dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+
+# DR EMBL; M36407; AAA33110.1; -.
+_fast_dbxref_sp_embl_data = None
+def _fast_dbxref_sp_embl(s):
+ global _fast_dbxref_sp_embl_data
+
+ if _fast_dbxref_sp_embl_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_embl_data = _fixup_sp_pattern(
+ sprot38.real_DR_embl)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_embl_data
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-embl dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+_fast_dbxref_parser_table = {
+ "sp-general": _fast_dbxref_sp_general,
+ "sp-prosite": _fast_dbxref_sp_prosite,
+ "sp-embl": _fast_dbxref_sp_embl,
+}
+
+class Handle_dbxref(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.supported_features.append("fast-sp-dbxref")
+ self.slow_callback = self.callback
+ def start_dbxref(self, tag, attrs):
+ self.negate = 0
+ self.dbname = None
+ self.dbids = []
+ self.info = []
+
+ def start_dbxref_dbname(self, tag, attrs):
+ assert self.dbname is None, "cannot set the dbname twice"
+ self.dbname_style = attrs.get("style", "unknown")
+ self.save_characters()
+ def end_dbxref_dbname(self, tag):
+ self.dbname = self.get_characters()
+
+ def start_dbxref_dbid(self, tag, attrs):
+ d = attrs.get("dbname", None)
+ if d is None:
+ assert self.dbname is not None, "must set the dbname"
+ self.info.append( (self.dbname_style, self.dbname,
+ attrs.get("type", "primary")) )
+ else:
+ self.info.append( ("bioformat", d,
+ attrs.get("type", "primary")) )
+ self.save_characters()
+
+ def end_dbxref_dbid(self, tag):
+ self.dbids.append( self.get_characters())
+
+ def start_dbxref_negate(self, tag, attrs):
+ self.negate = 1
+
+ def end_dbxref(self, tag):
+ cb = self.slow_callback
+ if cb is None:
+ return
+ negate = self.negate
+ for ( (dbname_style, dbname, idtype), dbid) in zip(self.info,
+ self.dbids):
+ self.slow_callback(dbname_style, dbname, idtype, dbid, negate)
+
+ def start_fast_dbxref(self, tag, attrs):
+ style = attrs["style"]
+ self._fast_parser = _fast_dbxref_parser_table[style]
+ self.save_characters()
+ self.slow_callback = None
+ def end_fast_dbxref(self, tag):
+ for info in self._fast_parser(self.get_characters()):
+ self.callback(*info)
+ self.slow_callback = self.callback
+
+##################
+class Handle_sequence(Dispatch.Callback):
+ global_alphabet = None
+ def start_(self, tag, attrs):
+ self.global_alphabet = None
+
+ def start_sequence_block(self, tag, attrs):
+ self.local_alphabet = attrs.get("alphabet", None)
+ self.gapchar = attrs.get("gapchar", None)
+ self.stopchar = attrs.get("stopchar", None)
+ j = attrs.get("join", None)
+ if j is not None:
+ self.join_func = Decode.make_typechecked_decoder(j, list, str)
+ else:
+ self.join_func = None
+ self.sequences = []
+
+ def end_sequence_block(self, tag):
+ f = self.join_func
+ if f is not None:
+ seq = self.f(self.sequences)
+ else:
+ seq = "".join(self.sequences).replace(" ", "")
+ alphabet = self.local_alphabet or self.global_alphabet or "unknown"
+ self.callback( (alphabet, seq, self.gapchar, self.stopchar) )
+
+ def start_alphabet(self, tag, attrs):
+ self.global_alphabet = attrs["alphabet"]
+
+ def start_sequence(self, tag, attrs):
+ self.save_characters()
+ def end_sequence(self, tag):
+ self.sequences.append(self.get_characters())
+
+class Feature:
+ def __init__(self, name, description, location, qualifiers):
+ self.name = name
+ self.description = description
+ self.location = location
+ self.qualifiers = qualifiers
+ def __str__(self):
+ return "Feature %r %r %s num_qualifiers = %d" % \
+ (self.name, self.description, self.location,
+ len(self.qualifiers))
+
+
+class Handle_feature_location(Dispatch.Callback):
+ def __init__(self, callback, settings = {}):
+ Dispatch.Callback.__init__(self, callback)
+ self.settings = settings
+
+ def start_feature(self, tag, attrs):
+ self.location_style = attrs.get("location-style",
+ self.settings["location-style"])
+ j = attrs.get("join-feature", None)
+ if j is None:
+ self.text_join_func = "".join
+ else:
+ self.text_join_func = Decode.make_typechecked_decoder(j, list, str)
+
+ self.location_start = None
+ self.location_end = None
+ self.text_lines = []
+
+ def end_feature(self, tag):
+ if self.location_start or self.location_end:
+ if self.text_lines:
+ raise TypeError("Cannot have both location text and start/end")
+ self.callback(self.location_style,
+ (self.location_start, self.location_end))
+ else:
+ self.callback(self.location_style,
+ (self.text_join_func(self.text_lines), None))
+
+ def start_feature_location(self, tag, attrs):
+ self.save_characters()
+ def end_feature_location(self, tag):
+ self.text_lines.append(self.get_characters())
+
+add_text_handler(Handle_feature_location, "feature_location_start",
+ "location_start")
+add_text_handler(Handle_feature_location, "feature_location_end",
+ "location_end")
+
+##################################
+
+class Handle_feature_qualifier(Dispatch.Callback):
+ def __init__(self, callback, settings):
+ self.settings = settings
+ Dispatch.Callback.__init__(self, callback)
+
+ def start_feature_qualifier(self, tag, attrs):
+ self.name = None
+ self.description = []
+ qj = attrs.get("join-qualifier", None)
+ if qj is None:
+ self.join = self.settings["qualifier_join_func"]
+ else:
+ self.join = Decode.make_typechecked_decoder(qj, list, str)
+
+ def end_feature_qualifier(self, tag):
+ self.callback(self.name, self.join(self.description))
+
+ def start_feature_qualifier_description(self, tag, attrs):
+ self.save_characters()
+ def end_feature_qualifier_description(self, tag):
+ self.description.append(self.get_characters())
+
+add_text_handler(Handle_feature_qualifier, "feature_qualifier_name", "name")
+
+####################
+
+class Handle_features(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.settings = {}
+
+ self.acquire(Handle_feature_location(self.add_location, self.settings))
+
+ self.acquire(Handle_feature_qualifier(self.add_feature_qualifier,
+ self.settings))
+
+ def start_feature_block(self, tag, attrs):
+ jf = attrs.get("join-description", None)
+ if jf is None:
+ self.join_feature_description = Decode.join_fixspaces
+ else:
+ self.join_feature_description = Decode.make_typechecked_decoder(
+ jf, list, str)
+
+ self.settings["location-style"] = attrs.get("location-style", None)
+
+ jq = attrs.get("join-qualifier", None)
+ if jq is None:
+ self.settings["qualifier_join_func"] = Decode.join_fixspaces
+ else:
+ self.settings["qualifier_join_func"] = \
+ Decode.make_typechecked_decoder(jq, list, str)
+ self.features = []
+
+ def end_feature_block(self, tag):
+ self.callback(self.features)
+ self.features = None
+
+ def start_feature(self, tag, attrs):
+ self.name = None
+ self.description = []
+ self.location = None
+ self.qualifiers = []
+
+ def start_feature_description(self, tag, attrs):
+ self.save_characters()
+ def end_feature_description(self, tag):
+ self.description.append(self.get_characters())
+
+ def end_feature(self, tag):
+ self.features.append(Feature(
+ self.name,
+ self.join_feature_description(self.description),
+ self.location,
+ self.qualifiers))
+
+ def add_feature_qualifier(self, name, description):
+ self.qualifiers.append((name, description))
+
+ def add_location(self, style, location_info):
+ self.location = (style, location_info)
+
+add_text_handler(Handle_features, "feature_name", "name")
+
+
+############## Search handlers
+
+class Handle_hsp_seqalign(Dispatch.Callback):
+ def start_hsp(self, tag, attrs):
+ self.query_name = None # "Query"
+ self.subject_name = None # "Sbjct"
+
+ self.query_seq = "" # the actual text of the sequence
+ self.homology_seq = ""
+ self.subject_seq = ""
+
+ self.query_start_loc = None
+ self.query_end_loc = None
+
+ self.subject_start_loc = None
+ self.subject_end_loc = None
+
+ def end_hsp(self, tag):
+ self.callback(self)
+
+ def start_hsp_seqalign(self, tag, attrs):
+ self.sub_leader = None
+
+ def start_hsp_seqalign_query_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_query_seq(self, tag):
+ s = self.get_characters()
+ self.query_seq += s
+ self.sub_query_seq_len = len(s)
+
+ def start_hsp_seqalign_homology_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_homology_seq(self, tag):
+ query_leader = self.leader_size
+ query_seq_len = self.sub_query_seq_len
+ line = self.get_characters()
+ s = line[query_leader:query_leader+query_seq_len]
+ assert len(s) == query_seq_len, (len(s), query_seq_len, line)
+ self.homology_seq += s
+
+ def start_hsp_seqalign_subject_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_subject_seq(self, tag):
+ self.subject_seq += self.get_characters()
+
+ def start_hsp_seqalign_query_leader(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_query_leader(self, tag):
+ self.leader_size = len(self.get_characters())
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_name",
+ "query_name")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_name",
+ "subject_name")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_start",
+ "query_start_loc")
+add_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_end",
+ "query_end_loc")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_start",
+ "subject_start_loc")
+add_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_end",
+ "subject_end_loc")
+
+
+
+
+#############################
+
+class Handle_hsp(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.acquire(Handle_hsp_seqalign(self.add_hsp_seqs))
+
+ def start_hsp(self, tag, attrs):
+ self.hsp_values = {} # expect, p, identities, ...
+ self.strands = {}
+ self.frames = {}
+
+ def end_hsp(self, tag):
+ self.callback(self.hsp_values,
+ self.hsp_info,
+ self.strands, self.frames,
+ )
+
+ def start_hsp_strand(self, tag, attrs):
+ self.strands[attrs["which"]] = attrs["strand"]
+
+ def start_hsp_frame(self, tag, attrs):
+ self.getting_frame = attrs["which"]
+ self.save_characters()
+
+ def end_hsp_frame(self, tag):
+ self.frames[self.getting_frame] = self.get_characters()
+ self.getting_frame = None
+
+ def add_hsp_seqs(self, hsp_info):
+ self.hsp_info = hsp_info
+
+ def start_hsp_value(self, tag, attrs):
+ self.value_convert = attrs.get("bioformat:decode", None)
+ self.value_name = attrs["name"]
+ self.save_characters()
+
+ def end_hsp_value(self, tag):
+ s = self.get_characters()
+ if self.value_name is not None:
+ if self.value_name == "float":
+ s = float(s)
+ else:
+ s = Decode.make_decoder(self.value_convert)(s)
+ self.hsp_values[self.value_name] = s
+
+#############################
+
+
+class Handle_search_table(Dispatch.Callback):
+ def start_search_table_value(self, tag, attrs):
+ self.value_name = attrs["name"]
+ self.value_decode = attrs.get("bioformat:decode", None)
+ self.save_characters()
+ def end_search_table_value(self, tag):
+ s = self.get_characters()
+ if self.value_decode is not None:
+ x = self.value_decode
+ if x == "int":
+ s = int(s)
+ elif x == "float":
+ s = float(s)
+ else:
+ s = Decode.make_decoder(x)(s)
+ self.values[self.value_name] = s
+
+ def start_search_table(self, tag, attrs):
+ self.data = []
+ def end_search_table(self, tag):
+ self.callback(self.data)
+ self.data = None
+
+ def start_search_table_entry(self, tag, attrs):
+ self.description = None
+ self.values = {}
+
+ def end_search_table_entry(self, tag):
+ self.data.append( (self.description, self.values) )
+ self.description = self.values = None
+
+add_text_handler(Handle_search_table, "search_table_description",
+ "description")
+
+#############################
+
+class Handle_search_header(Dispatch.Callback):
+ def start_(self, tag, attrs):
+ self.dict = {}
+ self.query_description = None
+
+ def end_search_header(self, tag):
+ d = self.dict
+ d["query_description"] = self.query_description
+ self.callback(d)
+
+add_text_block_handler(Handle_search_header, "query_description",
+ "join-query", "join|fixspaces", "query_description")
+
+add_text_dict_handler(Handle_search_header, "application_name",
+ "dict", "appname")
+add_text_dict_handler(Handle_search_header, "application_version",
+ "dict", "appversion")
+add_text_dict_handler(Handle_search_header, "database_name",
+ "dict", "dbname")
+add_text_dict_handler(Handle_search_header, "database_num_sequences",
+ "dict", "db_num_sequences")
+add_text_dict_handler(Handle_search_header, "database_num_letters",
+ "dict", "db_num_letters")
+add_text_dict_handler(Handle_search_header, "query_size",
+ "dict", "query_size")
+
+
+#############################
+
+class Handle_search_info(Dispatch.Callback):
+ def start_(self, tag, attrs):
+ self.parameters = {}
+ self.statistics = {}
+
+ def end_(self, tag):
+ self.callback(self.parameters, self.statistics)
+
+add_value_handler(Handle_search_info, "search_parameter", "parameters")
+add_value_handler(Handle_search_info, "search_statistic", "statistics")
--- /dev/null
+"""Code to transcribe DNA into RNA or back (OBSOLETE).
+
+You are now encouraged to use the Seq object methods or the functions
+in Bio.Seq instead.
+
+This module is now considered to be obsolete, and is likely to be deprecated
+in a future release of Biopython, and later removed.
+"""
+
+from Bio import Alphabet, Seq
+from Bio.Alphabet import IUPAC
+
+class Transcribe:
+ def __init__(self, dna_alphabet, rna_alphabet):
+ self.dna_alphabet = dna_alphabet
+ self.rna_alphabet = rna_alphabet
+
+ def transcribe(self, dna):
+ assert dna.alphabet == self.dna_alphabet, \
+ "transcribe has the wrong DNA alphabet"
+ s = dna.data
+ return Seq.Seq(s.replace("T", "U"), self.rna_alphabet)
+ def back_transcribe(self, rna):
+ assert rna.alphabet == self.rna_alphabet, \
+ "back transcribe has the wrong RNA alphabet"
+ s = rna.data
+ return Seq.Seq(s.replace("U", "T"), self.dna_alphabet)
+
+generic_transcriber = Transcribe(Alphabet.generic_dna,
+ Alphabet.generic_rna)
+ambiguous_transcriber = Transcribe(IUPAC.ambiguous_dna,
+ IUPAC.ambiguous_rna)
+unambiguous_transcriber = Transcribe(IUPAC.unambiguous_dna,
+ IUPAC.unambiguous_rna)
--- /dev/null
+"""Code to translate DNA or RNA into proteins (OBSOLETE).
+
+Instead of Bio.Translate, for translation you are now encouraged to use the
+Seq object's translate method, or the translate function in the Bio.Seq
+module. Translate-to-stop functionality is via an optional argument.
+
+Bio.Seq does not offer any back-translation function like the one here. It
+was concluded that a since a simple back-translation giving a Seq or python
+string could only capture some of the possible back translations, there were
+no practical uses for such a method/function.
+
+This module is now considered to be obsolete, and is likely to be deprecated
+in a future release of Biopython, and later removed.
+"""
+from Bio import Alphabet, Seq
+from Bio.Data import CodonTable
+
+class Translator:
+ def __init__(self, table):
+ self.table = table
+ self._encoded = {}
+
+ def __str__(self) :
+ return "Translator object\n" + str(self.table)
+
+ def translate(self, seq, stop_symbol = "*"):
+ #Allow different instances of the same class to be used:
+ assert seq.alphabet.__class__ == \
+ self.table.nucleotide_alphabet.__class__, \
+ "cannot translate from given alphabet (have %s, need %s)" %\
+ (seq.alphabet, self.table.nucleotide_alphabet)
+ s = seq.data
+ letters = []
+ append = letters.append
+ table = self.table
+ get = table.forward_table.get
+ n = len(seq)
+ for i in range(0, n-n%3, 3):
+ append(get(s[i:i+3], stop_symbol))
+
+ # return with the correct alphabet encoding (cache the encoding)
+ try:
+ alphabet = self._encoded[stop_symbol]
+ except KeyError:
+ alphabet = Alphabet.HasStopCodon(table.protein_alphabet,
+ stop_symbol)
+ self._encoded[stop_symbol] = alphabet
+
+ return Seq.Seq("".join(letters), alphabet)
+
+ def translate_to_stop(self, seq):
+ # This doesn't have a stop encoding
+
+ #Allow different instances of the same class to be used:
+ assert seq.alphabet.__class__ == \
+ self.table.nucleotide_alphabet.__class__, \
+ "cannot translate from given alphabet (have %s, need %s)" %\
+ (seq.alphabet, self.table.nucleotide_alphabet)
+ s = seq.data
+ letters = []
+ append = letters.append
+ table = self.table.forward_table
+ n = len(seq)
+ try:
+ for i in range(0, n-n%3, 3):
+ append(table[s[i:i+3]])
+ except KeyError:
+ # Stop at the first codon failure
+ pass
+ return Seq.Seq("".join(letters), self.table.protein_alphabet)
+
+ def back_translate(self, seq):
+ # includes the stop codon
+ if not isinstance(seq.alphabet, Alphabet.HasStopCodon):
+ return self._back_translate_no_stop(seq)
+ assert seq.alphabet.alphabet == self.table.protein_alphabet, \
+ "cannot back translate from the given alphabet (%s)" % \
+ seq.alphabet.alphabet
+ s = seq.data
+ letter = seq.alphabet.stop_symbol
+ letters = []
+ append = letters.append
+ table = self.table.back_table
+ for c in seq.data:
+ if c == letter:
+ append(table[None])
+ else:
+ append(table[c])
+ return Seq.Seq("".join(letters),
+ self.table.nucleotide_alphabet)
+
+ def _back_translate_no_stop(self, seq):
+ # does not allow a stop codon
+ assert seq.alphabet == self.table.protein_alphabet, \
+ "cannot back translate from the given alphabet (%s)" % \
+ seq.alphabet
+ s = seq.data
+ letters = []
+ append = letters.append
+ table = self.table.back_table
+ for c in seq.data:
+ append(table[c])
+ return Seq.Seq("".join(letters),
+ self.table.nucleotide_alphabet)
+
+unambiguous_dna_by_name = {}
+for key, value in CodonTable.unambiguous_dna_by_name.items():
+ unambiguous_dna_by_name[key] = Translator(value)
+unambiguous_dna_by_id = {}
+for key, value in CodonTable.unambiguous_dna_by_id.items():
+ unambiguous_dna_by_id[key] = Translator(value)
+
+unambiguous_rna_by_name = {}
+for key, value in CodonTable.unambiguous_rna_by_name.items():
+ unambiguous_rna_by_name[key] = Translator(value)
+unambiguous_rna_by_id = {}
+for key, value in CodonTable.unambiguous_rna_by_id.items():
+ unambiguous_rna_by_id[key] = Translator(value)
+
+# XXX Ambiguous - can be done the same except for stop codons!
+ambiguous_dna_by_name = {}
+for key, value in CodonTable.ambiguous_dna_by_name.items():
+ ambiguous_dna_by_name[key] = Translator(value)
+ambiguous_dna_by_id = {}
+for key, value in CodonTable.ambiguous_dna_by_id.items():
+ ambiguous_dna_by_id[key] = Translator(value)
+
+ambiguous_rna_by_name = {}
+for key, value in CodonTable.ambiguous_rna_by_name.items():
+ ambiguous_rna_by_name[key] = Translator(value)
+ambiguous_rna_by_id = {}
+for key, value in CodonTable.ambiguous_rna_by_id.items():
+ ambiguous_rna_by_id[key] = Translator(value)
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+
+import warnings
+warnings.warn("Bio.Writer and Bio.writer.* are deprecated. If you do use"\
+ +" these modules, please get in touch via the mailing list or"\
+ +" bugzilla to avoid their permanent removal from Biopython.", \
+ DeprecationWarning)
+
+class Writer:
+ def __init__(self, outfile):
+ self.outfile = outfile
+ def writeHeader(self):
+ pass
+ def write(self, record):
+ pass
+ def writeFooter(self):
+ pass
--- /dev/null
+# Copyright 2000 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+"""Collection of modules for dealing with biological data in Python.
+
+The Biopython Project is an international association of developers
+of freely available Python tools for computational molecular biology.
+
+http://biopython.org
+"""
+
+__version__ = "1.50"
+
+class MissingExternalDependencyError(Exception):
+ pass
--- /dev/null
+/* cMarkovModelmodule.c
+ * jchang
+ * Created: 1/13/01
+ * Last modified: 11/26/02
+ *
+ * This optimizes some of the functions in MarkovModel.py.
+ */
+
+#include "Python.h"
+#include "csupport.h"
+
+
+/* Functions in this module. */
+
+static char cMarkovModel__logadd__doc__[] =
+"_logadd(logx, logy) -> log(x+y)\n";
+
+static PyObject *cMarkovModel__logadd(PyObject *self, PyObject *args)
+{
+ PyObject *py_logx, *py_logy;
+ double logx, logy, minxy;
+ double sum;
+
+ if(!PyArg_ParseTuple(args, "OO", &py_logx, &py_logy))
+ return NULL;
+ logx = PyNumber_AsDouble(py_logx);
+ logy = PyNumber_AsDouble(py_logy);
+ if(PyErr_Occurred())
+ return NULL;
+
+ if(logy-logx > 100.0) {
+ Py_INCREF(py_logy);
+ return py_logy;
+ } else if (logx-logy > 100.0) {
+ Py_INCREF(py_logx);
+ return py_logx;
+ }
+ minxy = (logx < logy) ? logx : logy;
+ sum = minxy + log(exp(logx-minxy) + exp(logy-minxy));
+ return PyFloat_FromDouble(sum);
+}
+
+
+/* Module definition stuff */
+
+static PyMethodDef CMarkovModelMethods[] = {
+ {"_logadd", cMarkovModel__logadd, METH_VARARGS, cMarkovModel__logadd__doc__},
+ {NULL, NULL}
+};
+
+static char cMarkovModel__doc__[] =
+"This module provides optimized replacement functions for MarkovModel.\n\
+";
+
+void initcMarkovModel(void)
+{
+ Py_InitModule3("cMarkovModel", CMarkovModelMethods, cMarkovModel__doc__);
+}
+
+
+
--- /dev/null
+/* Copyright 2000 by Jeffrey Chang. All rights reserved.
+ * This code is part of the Biopython distribution and governed by its
+ * license. Please see the LICENSE file that should have been included
+ * as part of this package.
+ *
+ * clistfnsmodule.c
+ * Created 3 Jun 2000
+ */
+
+#include "Python.h"
+#include <math.h>
+
+
+
+
+/************************************** Exported Functions ***********/
+
+static char clistfns_count__doc__[] =
+"count(items) -> dict of counts of each item\n\
+\n\
+Count the number of times each item appears in a list of data.\n\
+\n\
+";
+
+static PyObject *clistfns_count(PyObject *self, PyObject *args)
+{
+ int i;
+ PyObject *items, *counts;
+ PyObject *item, *count, *newcount;
+ long int current;
+
+ if(!PyArg_ParseTuple(args, "O", &items))
+ return NULL;
+ if(!PySequence_Check(items)) {
+ PyErr_SetString(PyExc_TypeError, "expected sequence type");
+ return NULL;
+ }
+
+ if(!(counts = PyDict_New()))
+ return NULL;
+
+ /* Go through the loop, counting how often each item appears. */
+ i = 0;
+ while(1) {
+ if(!(item = PySequence_GetItem(items, i))) {
+ PyErr_Clear(); /* clear the exception set by PySequence_GetItem */
+ break; /* no more numbers */
+ }
+
+ if(!(count = PyDict_GetItem(counts, item))) {
+ newcount = PyInt_FromLong(1); /* New item, set count to 1 */
+ }
+ else {
+ current = PyInt_AsLong(count);
+ newcount = PyInt_FromLong(current+1);
+ }
+
+ PyDict_SetItem(counts, item, newcount);
+ Py_DECREF(newcount);
+ Py_DECREF(item);
+ if(PyErr_Occurred())
+ return NULL;
+
+ i++;
+ }
+
+ return counts;
+}
+
+
+static char clistfns_contents__doc__[] =
+"contents(items) -> dict of item -> percentage\n\
+\n\
+Summarize the contents of the list in terms of the percentages of each\n\
+item. For example, if an item appears 3 times in a list with 10 items,\n\
+it is in 0.3 of the list\n\
+\n\
+";
+
+static PyObject *clistfns_contents(PyObject *self, PyObject *args)
+{
+ int i;
+ PyObject *items, *counts, *percentages;
+ PyObject *countitems, *countitem;
+ PyObject *key, *count, *perc;
+ long c;
+ double total;
+
+ if(!PyArg_ParseTuple(args, "O", &items))
+ return NULL;
+ if(!PySequence_Check(items)) {
+ PyErr_SetString(PyExc_TypeError, "expected mapping type");
+ return NULL;
+ }
+ if((total = PySequence_Length(items)) == -1) {
+ PyErr_SetString(PyExc_ValueError, "I couldn't get length of item.");
+ return NULL;
+ }
+
+ counts = clistfns_count(self, args);
+ if(!counts || PyErr_Occurred())
+ return NULL;
+
+ if(!(percentages = PyDict_New())) {
+ Py_DECREF(counts);
+ return NULL;
+ }
+
+ /* Loop through every element in counts, calculating the probabilities. */
+ if(!(countitems = PyMapping_Items(counts))) {
+ Py_DECREF(counts);
+ Py_DECREF(percentages);
+ return NULL;
+ }
+
+ /* Go through the loop, counting how often each item appears. */
+ i = 0;
+ while(1) {
+ if(!(countitem = PyList_GetItem(countitems, i))) {
+ PyErr_Clear(); /* clear the exception set by PyList_GetItem */
+ break; /* no more numbers */
+ }
+ key = PyTuple_GetItem(countitem, 0);
+ count = PyTuple_GetItem(countitem, 1);
+ c = PyInt_AsLong(count);
+ perc = PyFloat_FromDouble((double)c / total);
+ PyDict_SetItem(percentages, key, perc);
+ Py_DECREF(perc);
+ if(PyErr_Occurred()) /* PyDict_SetItem failed */
+ break;
+ i++;
+ }
+ if(PyErr_Occurred()) {
+ Py_DECREF(percentages);
+ percentages = NULL;
+ }
+ Py_DECREF(countitems);
+ Py_DECREF(counts);
+
+ return percentages;
+}
+
+
+/************************************** Module definition stuff ******/
+
+static PyMethodDef clistfnsMethods[] = {
+ {"count", clistfns_count, METH_VARARGS, clistfns_count__doc__},
+ {"contents", clistfns_contents, METH_VARARGS, clistfns_contents__doc__},
+ {NULL, NULL}
+};
+
+static char clistfns__doc__[] =
+"This provides helper functions for the listfns module.\n\
+You should never import this module on its own.\n\
+\n\
+";
+
+void initclistfns(void)
+{
+ (void) Py_InitModule3("clistfns", clistfnsMethods, clistfns__doc__);
+}
--- /dev/null
+/* Copyright 2000 by Jeffrey Chang. All rights reserved.
+ * This code is part of the Biopython distribution and governed by its
+ * license. Please see the LICENSE file that should have been included
+ * as part of this package.
+ *
+ * cmathfnsmodule.c
+ * Created 3 Jun 2000
+ */
+
+#include "Python.h"
+#include <math.h>
+
+#include "csupport.h"
+
+
+
+/************************************** Exported Functions ***********/
+
+static char cmathfns_intd__doc__[] =
+"intd(x[, digits_after_decimal]) -> int x, rounded\n\
+\n\
+Represent a floating point number with some digits after the\n\
+decimal point as an integer. This is useful when floating point\n\
+comparisons are failing due to precision problems. e.g.\n\
+intd(5.35, 1) -> 54.\n\
+\n\
+";
+
+static PyObject *cmathfns_intd(
+ PyObject *self, PyObject *args, PyObject *keywds)
+{
+ PyObject *digits_after_decimal = Py_None;
+ double x, digits;
+ double precision;
+
+ static char *kwlist[] = {"x", "digits_after_decimal", NULL};
+ if(!PyArg_ParseTupleAndKeywords(args, keywds, "d|O", kwlist,
+ &x, &digits_after_decimal))
+ return NULL;
+
+ if(digits_after_decimal == Py_None)
+ digits = 0;
+ else {
+ digits = PyNumber_AsDouble(digits_after_decimal);
+ if(PyErr_Occurred()) {
+ return NULL;
+ }
+ }
+ precision = pow(10, digits);
+ if(x >= 0)
+ x = (int)(x * precision + 0.5);
+ else
+ x = (int)(x * precision - 0.5);
+ return PyFloat_FromDouble(x);
+}
+
+
+
+
+static char cmathfns_fcmp__doc__[] =
+"fcmp(x, y, precision) -> -1, 0, or 1";
+
+static PyObject *cmathfns_fcmp(
+ PyObject *self, PyObject *args, PyObject *keywds)
+{
+ double x, y, precision;
+ int result;
+
+ static char *kwlist[] = {"x", "y", "precision", NULL};
+ if(!PyArg_ParseTupleAndKeywords(args, keywds, "ddd", kwlist,
+ &x, &y, &precision))
+ return NULL;
+
+ if(fabs(x-y) < precision)
+ result = 0;
+ else if(x < y)
+ result = -1;
+ else result = 1;
+ return PyInt_FromLong(result);
+}
+
+
+
+static char cmathfns_safe_log__doc__[] =
+"safe_log(n, zero=None, neg=None) -> log(n)\n\
+\n\
+Calculate the log of n. If n is 0, returns the value of zero. If n is\n\
+negative, returns the value of neg.\n\
+\n\
+";
+
+static PyObject *cmathfns_safe_log(
+ PyObject *self, PyObject *args, PyObject *keywds)
+{
+ PyObject *zero = Py_None,
+ *neg = Py_None;
+ double n;
+
+ static char *kwlist[] = {"n", "zero", "neg", NULL};
+
+ if(!PyArg_ParseTupleAndKeywords(args, keywds, "d|OO", kwlist,
+ &n, &zero, &neg))
+ return NULL;
+
+ if(n < 0) {
+ Py_INCREF(neg);
+ return neg;
+ } else if(n < 1E-100) {
+ Py_INCREF(zero);
+ return zero;
+ }
+
+ return PyFloat_FromDouble(log(n));
+}
+
+
+
+
+/************************************** Module definition stuff ******/
+
+static PyMethodDef cmathfnsMethods[] = {
+ {"fcmp", (PyCFunction)cmathfns_fcmp, METH_VARARGS|METH_KEYWORDS,
+ cmathfns_fcmp__doc__},
+ {"intd", (PyCFunction)cmathfns_intd, METH_VARARGS|METH_KEYWORDS,
+ cmathfns_intd__doc__},
+ {"safe_log", (PyCFunction)cmathfns_safe_log, METH_VARARGS|METH_KEYWORDS,
+ cmathfns_safe_log__doc__},
+ {NULL, NULL}
+};
+
+static char cmathfns__doc__[] =
+"This provides helper functions for the mathfns module.\n\
+You should never import this module on its own.\n\
+\n\
+";
+
+void initcmathfns(void)
+{
+ (void) Py_InitModule3("cmathfns", cmathfnsMethods, cmathfns__doc__);
+}
--- /dev/null
+/* Copyright 2000 by Jeffrey Chang. All rights reserved.
+ * This code is part of the Biopython distribution and governed by its
+ * license. Please see the LICENSE file that should have been included
+ * as part of this package.
+ *
+ * cstringfnsmodule.c
+ * Created 7 Jun 2000
+ */
+
+#include "Python.h"
+#include <string.h> /* memset */
+
+
+/* Functions in this module. */
+
+static char cstringfns_splitany__doc__[] =
+"splitany(str [,sep [,maxsplit [,negate]]]) -> list of strings\n\
+\n\
+Split a string. Similar to string.split, except that this considers\n\
+any one of the characters in sep to be a delimiter. If negate is\n\
+true, then everything but sep will be a separator.\n\
+\n\
+";
+
+static PyObject *cstringfns_splitany(
+ PyObject *self, PyObject *args, PyObject *keywds)
+{
+ int i, prev;
+ int nsplit, maxsplit=0;
+ /*int negate=0;*/
+ PyObject *py_negate=NULL;
+ PyObject *strlist, *newstr;
+ unsigned char *str,
+ *sep=" \011\012\013\014\015"; /* whitespace */
+ char tosplit[256];
+ static char *kwlist[] = {"str", "sep", "maxsplit", "negate", NULL};
+
+ if(!PyArg_ParseTupleAndKeywords(args, keywds, "s|siO", kwlist,
+ &str, &sep, &maxsplit, &py_negate))
+ return NULL;
+ if(maxsplit < 0)
+ maxsplit = 1;
+ /* negate = (py_negate && PyObject_IsTrue(py_negate));*/
+ /* XXX NO MORE NEGATE */
+
+ /* Set the tosplit array to 1 for characters to split on. */
+ memset(tosplit, 0, 256);
+ while(*sep) {
+ tosplit[(unsigned char)*sep++] = 1;
+ }
+ if(py_negate && PyObject_IsTrue(py_negate)) {
+ for(i=0; i<256; i++)
+ tosplit[i] = !tosplit[i];
+ }
+
+ /* Create a new list to store the variables. */
+ if(!(strlist = PyList_New(0))) {
+ PyErr_SetString(PyExc_SystemError, "I could not create a new list");
+ return NULL;
+ }
+
+ prev = 0;
+ nsplit = 0;
+ for(i=0; str[i] && (maxsplit == 0 || nsplit < maxsplit); i++) {
+ /*if(!(tosplit[(int)str[i]] == !negate))
+ continue; */
+ if(!tosplit[(int)str[i]])
+ continue;
+
+ /* Split the string here. */
+ if(!(newstr = PyString_FromStringAndSize(&str[prev], i-prev))) {
+ PyErr_SetString(PyExc_SystemError,
+ "I could not create a new string");
+ break;
+ }
+ if(PyList_Append(strlist, newstr) == -1) {
+ Py_DECREF(newstr);
+ break;
+ }
+ Py_DECREF(newstr);
+ prev = i+1;
+ nsplit++;
+ }
+ if(!PyErr_Occurred()) {
+ i = strlen(str);
+ /* Add the last one. */
+ if(!(newstr = PyString_FromStringAndSize(&str[prev], i-prev))) {
+ PyErr_SetString(PyExc_SystemError,
+ "I could not create a new string");
+ } else {
+ PyList_Append(strlist, newstr);
+ Py_DECREF(newstr);
+ }
+ } else {
+ Py_DECREF(strlist);
+ return NULL;
+ }
+
+
+ return strlist;
+}
+
+
+
+/* Module definition stuff */
+
+static PyMethodDef cstringfnsMethods[] = {
+ {"splitany", (PyCFunction)cstringfns_splitany, METH_VARARGS|METH_KEYWORDS,
+ cstringfns_splitany__doc__},
+ {NULL, NULL}
+};
+
+static char cstringfns__doc__[] =
+"This provides helper functions for the stringfns module.\n\
+You should never import this module on its own.\n\
+\n\
+";
+
+void initcstringfns(void)
+{
+ (void) Py_InitModule3("cstringfns", cstringfnsMethods, cstringfns__doc__);
+}
--- /dev/null
+/* Copyright 2002 by Jeffrey Chang. All rights reserved.
+ * This code is part of the Biopython distribution and governed by its
+ * license. Please see the LICENSE file that should have been included
+ * as part of this package.
+ *
+ * csupport.c
+ * Created 27 January 2002
+ *
+ * Miscellaneous useful C functions not to be exported as a python
+ * module.
+ *
+ */
+
+#include "Python.h"
+
+
+/* Return a PyNumber as a double.
+ * Raises a TypeError if I can't do it.
+ */
+double PyNumber_AsDouble(PyObject *py_num)
+{
+ double val;
+ PyObject *floatobj;
+
+ if((floatobj = PyNumber_Float(py_num)) == NULL)
+ return(0.0);
+ val = PyFloat_AsDouble(floatobj);
+ Py_DECREF(floatobj);
+ return val;
+}
--- /dev/null
+
+double PyNumber_AsDouble(PyObject *py_num);
--- /dev/null
+"""
+This module provides code for various distance measures.
+
+Functions:
+euclidean Euclidean distance between two points
+euclidean_py Pure Python implementation of euclidean.
+
+"""
+# XXX cosine distance
+
+import warnings
+warnings.warn("Bio.distance is deprecated. If you use this module, please notify the Biopython developers at biopython-dev@biopython.org", DeprecationWarning)
+
+from numpy import *
+
+def euclidean(x, y):
+ """euclidean(x, y) -> euclidean distance between x and y"""
+ if len(x) != len(y):
+ raise ValueError("vectors must be same length")
+ #return sqrt(sum((x-y)**2))
+ # Optimization by John Corradi (JCorradi@msn.com)
+ d = x-y
+ return sqrt(dot(d, d))
+
+def euclidean_py(x, y):
+ """euclidean_py(x, y) -> euclidean distance between x and y"""
+ # lightly modified from implementation by Thomas Sicheritz-Ponten.
+ # This works faster than the Numeric implementation on shorter
+ # vectors.
+ if len(x) != len(y):
+ raise ValueError("vectors must be same length")
+ sum = 0
+ for i in range(len(x)):
+ sum += (x[i]-y[i])**2
+ return sqrt(sum)
--- /dev/null
+#!/usr/bin/env python
+
+"""
+This module provides code for doing k-nearest-neighbors classification.
+
+k Nearest Neighbors is a supervised learning algorithm that classifies
+a new observation based the classes in its surrounding neighborhood.
+
+Glossary:
+distance The distance between two points in the feature space.
+weight The importance given to each point for classification.
+
+
+Classes:
+kNN Holds information for a nearest neighbors classifier.
+
+
+Functions:
+train Train a new kNN classifier.
+calculate Calculate the probabilities of each class, given an observation.
+classify Classify an observation into a class.
+
+ Weighting Functions:
+equal_weight Every example is given a weight of 1.
+
+"""
+
+#TODO - Remove this work around once we drop python 2.3 support
+try:
+ set = set
+except NameError:
+ from sets import Set as set
+
+import numpy
+
+class kNN:
+ """Holds information necessary to do nearest neighbors classification.
+
+ Members:
+ classes Set of the possible classes.
+ xs List of the neighbors.
+ ys List of the classes that the neighbors belong to.
+ k Number of neighbors to look at.
+
+ """
+ def __init__(self):
+ """kNN()"""
+ self.classes = set()
+ self.xs = []
+ self.ys = []
+ self.k = None
+
+def equal_weight(x, y):
+ """equal_weight(x, y) -> 1"""
+ # everything gets 1 vote
+ return 1
+
+def train(xs, ys, k, typecode=None):
+ """train(xs, ys, k) -> kNN
+
+ Train a k nearest neighbors classifier on a training set. xs is a
+ list of observations and ys is a list of the class assignments.
+ Thus, xs and ys should contain the same number of elements. k is
+ the number of neighbors that should be examined when doing the
+ classification.
+
+ """
+ knn = kNN()
+ knn.classes = set(ys)
+ knn.xs = numpy.asarray(xs, typecode)
+ knn.ys = ys
+ knn.k = k
+ return knn
+
+def calculate(knn, x, weight_fn=equal_weight, distance_fn=None):
+ """calculate(knn, x[, weight_fn][, distance_fn]) -> weight dict
+
+ Calculate the probability for each class. knn is a kNN object. x
+ is the observed data. weight_fn is an optional function that
+ takes x and a training example, and returns a weight. distance_fn
+ is an optional function that takes two points and returns the
+ distance between them. If distance_fn is None (the default), the
+ Euclidean distance is used. Returns a dictionary of the class to
+ the weight given to the class.
+
+ """
+ x = numpy.asarray(x)
+
+ order = [] # list of (distance, index)
+ if distance_fn:
+ for i in range(len(knn.xs)):
+ dist = distance_fn(x, knn.xs[i])
+ order.append((dist, i))
+ else:
+ # Default: Use a fast implementation of the Euclidean distance
+ temp = numpy.zeros(len(x))
+ # Predefining temp allows reuse of this array, making this
+ # function about twice as fast.
+ for i in range(len(knn.xs)):
+ temp[:] = x - knn.xs[i]
+ dist = numpy.sqrt(numpy.dot(temp,temp))
+ order.append((dist, i))
+ order.sort()
+
+ # first 'k' are the ones I want.
+ weights = {} # class -> number of votes
+ for k in knn.classes:
+ weights[k] = 0.0
+ for dist, i in order[:knn.k]:
+ klass = knn.ys[i]
+ weights[klass] = weights[klass] + weight_fn(x, knn.xs[i])
+
+ return weights
+
+def classify(knn, x, weight_fn=equal_weight, distance_fn=None):
+ """classify(knn, x[, weight_fn][, distance_fn]) -> class
+
+ Classify an observation into a class. If not specified, weight_fn will
+ give all neighbors equal weight. distance_fn is an optional function
+ that takes two points and returns the distance between them. If
+ distance_fn is None (the default), the Euclidean distance is used.
+ """
+ weights = calculate(
+ knn, x, weight_fn=weight_fn, distance_fn=distance_fn)
+
+ most_class = None
+ most_weight = None
+ for klass, weight in weights.items():
+ if most_class is None or weight > most_weight:
+ most_class = klass
+ most_weight = weight
+ return most_class
--- /dev/null
+# Copyright 2000 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""This provides useful general functions for working with lists (OBSOLETE).
+
+This module and its C code equivalent are considered to be obsolete, and
+are likely to be deprecated in a future release of Biopython, before being
+removed. Please get in touch via the mailing list if this will affect you.
+Many of these functions can be avoided using the python set object.
+
+Functions:
+asdict Make the list into a dictionary (for fast testing of membership).
+items Get one of each item in a list.
+count Count the number of times each item appears.
+contents Calculate percentage each item appears in a list.
+itemindex Make an index of the items in the list.
+intersection Get the items in common between 2 lists.
+difference Get the items in 1 list, but not the other.
+indexesof Get a list of the indexes of some items in a list.
+take Take some items from a list.
+
+"""
+
+def asdict(l):
+ """asdict(l) -> dictionary
+
+ Return a dictionary where the keys are the items in the list, with
+ arbitrary values. This is useful for quick testing of membership.
+
+ """
+ return count(l)
+
+def items(l):
+ """items(l) -> list of items
+
+ Generate a list of one of each item in l. The items are returned
+ in arbitrary order.
+
+ """
+ try:
+ return asdict(l).keys()
+ except TypeError, x:
+ if str(x).find("unhashable") == -1:
+ raise
+ # asdict failed because l is unhashable. Back up to a naive
+ # implementation.
+ l = l[:]
+ l.sort()
+ i = 0
+ while i < len(l)-1:
+ if l[i] == l[i+1]:
+ del l[i]
+ else:
+ i += 1
+ return l
+
+def count(items):
+ """count(items) -> dict of counts of each item
+
+ Count the number of times each item appears in a list of data.
+
+ """
+ c = {}
+ for i in items:
+ c[i] = c.get(i, 0) + 1
+ return c
+
+def contents(items):
+ """contents(items) -> dict of item:percentage
+
+ Summarize the contents of the list in terms of the percentages of each
+ item. For example, if an item appears 3 times in a list with 10 items,
+ it is in 0.3 of the list.
+
+ """
+ counts = count(items)
+ l = float(len(items))
+ contents = {}
+ for i, c in counts.items():
+ contents[i] = c / l
+ return contents
+
+def intersection(l1, l2):
+ """intersection(l1, l2) -> list of common items
+
+ Return a list of the items in both l1 and l2. The list is in
+ arbitrary order.
+
+ """
+ inter = []
+ words1 = count(l1)
+ for w in l2:
+ if words1.has_key(w):
+ inter.append(w)
+ del words1[w] # don't add the same word twice
+ return inter
+
+def difference(l1, l2):
+ """difference(l1, l2) -> list of items in l1, but not l2
+
+ Return a list of the items in l1, but not l2. The list is in
+ arbitrary order.
+
+ """
+ diff = []
+ words2 = count(l2)
+ for w in l1:
+ if not words2.has_key(w):
+ diff.append(w)
+ words2[w] = 1 # don't add the same word twice
+ return diff
+
+def itemindex(l):
+ """itemindex(l) -> dict of item : index of item
+
+ Make an index of the items in the list. The dictionary contains
+ the items in the list as the keys, and the index of the first
+ occurrence of the item as the value.
+
+ """
+ dict = {}
+ for i in range(len(l)):
+ if not dict.has_key(l[i]):
+ dict[l[i]] = i
+ return dict
+
+def indexesof(l, fn, opposite=0):
+ """indexesof(l, fn) -> list of indexes
+
+ Return a list of indexes i where fn(l[i]) is true.
+
+ """
+ indexes = []
+ for i in range(len(l)):
+ f = fn(l[i])
+ if (not opposite and f) or (opposite and not f):
+ indexes.append(i)
+ return indexes
+
+def take(l, indexes):
+ """take(l, indexes) -> list of just the indexes from l"""
+ items = []
+ for i in indexes:
+ items.append(l[i])
+ return items
+
+def take_byfn(l, fn, opposite=0):
+ indexes = indexesof(l, fn, opposite=opposite)
+ return take(l, indexes)
+
+# Try and load C implementations of functions. If I can't,
+# then just ignore and use the pure python implementations.
+try:
+ from clistfns import *
+except ImportError:
+ pass
--- /dev/null
+# Copyright 2000 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""This provides useful general math tools (DEPRECATED).
+
+This module and its C code equivalent are considered to be deprecated, and
+are likely to be removed in a future release of Biopython. Please get in
+touch via the mailing list if this will affect you.
+
+Functions:
+fcmp Compare two floating point numbers, up to a specified precision.
+intd Represent a floating point number as an integer.
+safe_log log, but returns an arbitrarily small number for log(0).
+safe_exp exp, but returns a large or small number instead of overflows.
+
+"""
+import warnings
+warnings.warn("Bio.mathfns and its C code equivalent Bio.cmathfns are" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+
+import math
+
+def fcmp(x, y, precision):
+ """fcmp(x, y, precision) -> -1, 0, or 1"""
+ if math.fabs(x-y) < precision:
+ return 0
+ elif x < y:
+ return -1
+ return 1
+
+def intd(x, digits_after_decimal=0):
+ """intd(x[, digits_after_decimal]) -> int x, rounded
+
+ Represent a floating point number with some digits after the
+ decimal point as an integer. This is useful when floating point
+ comparisons are failing due to precision problems. e.g.
+ intd(5.35, 1) -> 54.
+
+ """
+ precision = 10.**digits_after_decimal
+ if x >= 0:
+ x = int(x * precision + 0.5)
+ else:
+ x = int(x * precision - 0.5)
+ return x
+
+def safe_log(n, zero=None, neg=None):
+ """safe_log(n, zero=None, neg=None) -> log(n)
+
+ Calculate the log of n. If n is 0, returns the value of zero. If n is
+ negative, returns the value of neg.
+
+ """
+ if n < 0:
+ return neg
+ elif n < 1E-100:
+ return zero
+ return math.log(n)
+
+LOG2 = math.log(2)
+def safe_log2(n, zero=None, neg=None):
+ """safe_log2(n, zero=None, neg=None) -> log(n)
+
+ Calculate the log base 2 of n. If n is 0, returns the value of
+ zero. If n is negative, returns the value of neg.
+
+ """
+ l = safe_log(n, zero=zero, neg=neg)
+ if l is None:
+ return l
+ return l/LOG2
+
+def safe_exp(n, under=None, over=None):
+ """safe_exp(n, under=None, over=None) -> e**n
+
+ Guaranteed not to overflow. Instead of overflowing, it returns
+ the values of 'under' for underflows or 'over' for overflows.
+
+ """
+ try:
+ return math.exp(n)
+ except OverflowError:
+ if n < 0:
+ return under
+ return over
+ raise "How did I get here?"
+
+# Try and load C implementations of functions. If I can't,
+# then just ignore and use the pure python implementations.
+try:
+ from cmathfns import *
+except ImportError:
+ pass
--- /dev/null
+# Copyright 2000 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""This provides useful general functions for working with strings (DEPRECATED).
+
+This module and its C code equivalent are considered to be deprecated, and
+are likely to be removed in a future release of Biopython. Please get in
+touch via the mailing list if this will affect you.
+
+Functions:
+splitany Split a string using many delimiters.
+find_anychar Find one of a list of characters in a string.
+rfind_anychar Find one of a list of characters in a string, from end to start.
+
+"""
+import warnings
+warnings.warn("Bio.stringfns and its C code equivalent Bio.cstringfns are" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+
+def splitany(s, sep=" \011\012\013\014\015", maxsplit=None, negate=0):
+ """splitany(s [,sep [,maxsplit [,negate]]]) -> list of strings
+
+ Split a string. Similar to string.split, except that this considers
+ any one of the characters in sep to be a delimiter. If negate is
+ true, then everything but sep will be a separator.
+
+ """
+ strlist = []
+ prev = 0
+ for i in range(len(s)):
+ if maxsplit is not None and len(strlist) >= maxsplit:
+ break
+ if (s[i] in sep) == (not negate):
+ strlist.append(s[prev:i])
+ prev = i+1
+ strlist.append(s[prev:])
+ return strlist
+
+def find_anychar(string, chars, index=None, negate=0):
+ """find_anychar(string, chars[, index]) -> index of a character or -1
+
+ Find a character in string. chars is a list of characters to look
+ for. Return the index of the first occurrence of any of the
+ characters, or -1 if not found. index is the index where the
+ search should start. By default, I search from the beginning of
+ the string.
+
+ """
+ if index is None:
+ index = 0
+ while index < len(string) and \
+ ((not negate and string[index] not in chars) or
+ (negate and string[index] in chars)):
+ index += 1
+ if index == len(string):
+ return -1
+ return index
+
+def rfind_anychar(string, chars, index=None, negate=0):
+ """rfind_anychar(string, chars[, index]) -> index of a character or -1
+
+ Find a character in string, looking from the end to the start.
+ chars is a list of characters to look for. Return the index of
+ the first occurrence of any of the characters, or -1 if not found.
+ index is the index where the search should start. By default, I
+ search from the end of the string.
+
+ """
+ if index is None:
+ index = len(string)-1
+ while index >= 0 and \
+ ((not negate and string[index] not in chars) or
+ (negate and string[index] in chars)):
+ index -= 1
+ # If not found, index will already be -1.
+ return index
+
+# Try and load C implementations of functions. If I can't,
+# then just ignore and use the pure python implementations.
+try:
+ from cstringfns import *
+except ImportError:
+ pass
--- /dev/null
+#include <stdio.h> /* printf */
+#include <stdlib.h> /* malloc */
+#include <string.h> /* strcmp, strlen */
+
+#include "trie.h"
+
+/* The following is necessary to make sure that trie.pyd won't link
+ * to msvcrt.dll in addition to msvcr71.dll on Windows.
+ * See Bug #1767 on Bugzilla.
+ */
+#ifdef __MINGW32__
+# define strdup _strdup
+#endif
+
+struct _Transition; /* Forward declaration, needed in _Trie. */
+
+
+/* _Trie is a recursive data structure. A _Trie contains zero or more
+ * _Transitions that lead to more _Tries. The transitions are stored
+ * in alphabetical order of the suffix member of the data structure.
+ * _Trie also contains a pointer called value where the user can store
+ * arbitrary data. If value is NULL, then no data is stored here.
+ */
+struct _Trie {
+ struct _Transition *transitions;
+ unsigned char num_transitions;
+ void *value; /* specified by user, never freed or allocated by me! */
+};
+
+/* _Transition holds information about the transitions leading from
+ * one _Trie to another. The trie structure here is different from
+ * typical ones, because the transitions between nodes can contain
+ * strings of arbitrary length, not just single characters. Suffix is
+ * the string that is matched from one node to the next.
+ */
+typedef struct _Transition {
+ unsigned char *suffix;
+ Trie next;
+} *Transition;
+
+
+#define MAX_KEY_LENGTH 1000
+static unsigned char KEY[MAX_KEY_LENGTH];
+
+
+Trie Trie_new(void) {
+ Trie trie;
+
+ if(!(trie = (Trie)malloc(sizeof(struct _Trie))))
+ return NULL;
+ trie->transitions = NULL;
+ trie->num_transitions = 0;
+ trie->value = NULL;
+ return trie;
+}
+
+int Trie_set(Trie trie, const unsigned char *key, const void *value) {
+ int i;
+ Transition transition=NULL;
+ unsigned char *suffix=NULL;
+ int retval = 0;
+ int first, last, mid;
+
+ if(!key[0]) {
+ trie->value = (void *)value;
+ return 0;
+ }
+
+ /* Insert the key in alphabetical order. Do a binary search to
+ find the proper place. */
+ first = 0;
+ last = trie->num_transitions-1;
+ i = -1;
+ while(first <= last) {
+ mid = (first+last)/2;
+ transition = &trie->transitions[mid];
+ suffix = transition->suffix;
+ if(key[0] < suffix[0])
+ last = mid-1;
+ else if(key[0] > suffix[0])
+ first = mid+1;
+ else {
+ i = mid;
+ break;
+ }
+ }
+
+ /* If no place was found for it, then the indexes will be in the
+ order last,first. Place it at index first. */
+ if(i == -1)
+ i = first;
+
+ /* If nothing matches, then insert a new trie here. */
+ if((i >= trie->num_transitions) || (key[0] != suffix[0])) {
+ unsigned char *new_suffix=NULL;
+ Trie newtrie=NULL;
+ Transition new_transitions=NULL;
+
+ /* Create some variables for the new transition. I'm going to
+ allocate these first so that if I can detect memory errors
+ before I mess up the data structure of the transitions.
+ */
+ if(!(new_suffix = (unsigned char *)strdup(key)))
+ goto insert_memerror;
+ if(!(newtrie = Trie_new()))
+ goto insert_memerror;
+
+ /* Create some space for the next transition. Allocate some
+ memory and shift the old transitions over to make room for
+ this one.
+ */
+ if(!(new_transitions = malloc(sizeof(struct _Transition) *
+ (trie->num_transitions+1))))
+ goto insert_memerror;
+ memcpy(new_transitions, trie->transitions,
+ sizeof(struct _Transition)*i);
+ memcpy(&new_transitions[i+1], &trie->transitions[i],
+ sizeof(struct _Transition)*(trie->num_transitions-i));
+ free(trie->transitions);
+ trie->transitions = new_transitions;
+ new_transitions = NULL;
+ trie->num_transitions += 1;
+
+ /* Initialize the new transition. */
+ transition = &trie->transitions[i];
+ transition->suffix = new_suffix;
+ transition->next = newtrie;
+ transition->next->value = (void *)value;
+
+ if(0) {
+ insert_memerror:
+ if(new_transitions) free(new_transitions);
+ if(newtrie) free(newtrie);
+ if(new_suffix) free(new_suffix);
+ return 1;
+ }
+ }
+ /* There are three cases where the key and suffix share some
+ letters.
+ 1. suffix is proper substring of key.
+ 2. key is proper substring of suffix.
+ 3. neither is proper substring of other.
+
+ For cases 2 and 3, I need to first split up the transition
+ based on the number of characters shared. Then, I can insert
+ the rest of the key into the next trie.
+ */
+ else {
+ /* Count the number of characters shared between key
+ and suffix. */
+ int chars_shared = 0;
+ while(key[chars_shared] && key[chars_shared] == suffix[chars_shared])
+ chars_shared++;
+
+ /* Case 2 or 3, split this sucker! */
+ if(chars_shared < strlen(suffix)) {
+ Trie newtrie=NULL;
+ unsigned char *new_suffix1=NULL, *new_suffix2=NULL;
+
+ if(!(new_suffix1 = (unsigned char *)malloc(chars_shared+1)))
+ goto split_memerror;
+ strncpy(new_suffix1, key, chars_shared);
+ new_suffix1[chars_shared] = 0;
+ if(!(new_suffix2 = (unsigned char *)strdup(suffix+chars_shared)))
+ goto split_memerror;
+ if(!(newtrie = Trie_new()))
+ goto split_memerror;
+ if(!(newtrie->transitions =
+ (Transition)malloc(sizeof(struct _Transition))))
+ goto split_memerror;
+ newtrie->num_transitions = 1;
+ newtrie->transitions[0].next = transition->next;
+ newtrie->transitions[0].suffix = new_suffix2;
+
+ free(transition->suffix);
+ transition->suffix = new_suffix1;
+ transition->next = newtrie;
+
+ if(0) {
+ split_memerror:
+ if(newtrie && newtrie->transitions) free(newtrie->transitions);
+ if(newtrie) free(newtrie);
+ if(new_suffix2) free(new_suffix2);
+ if(new_suffix1) free(new_suffix1);
+ return 1;
+ }
+ }
+ retval = Trie_set(transition->next, key+chars_shared, value);
+ }
+
+ return retval;
+}
+
+void Trie_del(Trie trie) {
+ int i;
+ if(!trie)
+ return;
+ for(i=0; i<trie->num_transitions; i++) {
+ Transition transition = &trie->transitions[i];
+ if(transition->suffix)
+ free(transition->suffix);
+ Trie_del(transition->next);
+ }
+ free(trie);
+}
+
+void *Trie_get(const Trie trie, const unsigned char *key) {
+ int first, last, mid;
+
+ if(!key[0]) {
+ return trie->value;
+ }
+
+ /* The transitions are stored in alphabetical order. Do a binary
+ * search to find the proper one.
+ */
+ first = 0;
+ last = trie->num_transitions-1;
+ while(first <= last) {
+ Transition transition;
+ unsigned char *suffix;
+ int c;
+ mid = (first+last)/2;
+ transition = &trie->transitions[mid];
+ suffix = transition->suffix;
+ /* If suffix is a substring of key, then get the value from
+ the next trie.
+ */
+ c = strncmp(key, suffix, strlen(suffix));
+ if(c < 0)
+ last = mid-1;
+ else if(c > 0)
+ first = mid+1;
+ else
+ return Trie_get(transition->next, key+strlen(suffix));
+ }
+ return NULL;
+}
+
+
+/* Mutually recursive, so need to make a forward declaration. */
+void
+_get_approximate_trie(const Trie trie, const unsigned char *key, const int k,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ const int mismatches,
+ void *data),
+ void *data,
+ const int mismatches,
+ unsigned char *current_key, const int max_key
+ );
+
+void
+_get_approximate_transition(const unsigned char *key,
+ const int k,
+ const Transition transition,
+ const unsigned char *suffix,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ const int mismatches,
+ void *data),
+ void *data,
+ const int mismatches,
+ unsigned char *current_key, const int max_key
+ )
+{
+ int i;
+ int prev_keylen = strlen(current_key);
+
+ /* Short circuit optimization. If there's too many characters to
+ possibly be a match, then don't even try to match things. */
+ if((int)(strlen(suffix) - strlen(key)) > k)
+ return;
+
+ /* Match as many characters as possible. */
+ i = 0;
+ while(suffix[i] && (key[i] == suffix[i])) {
+ i++;
+ }
+ /* Check to make sure the key is not too long. BUG: If it is,
+ fails silently. */
+ if((prev_keylen+i) >= max_key)
+ return;
+ strncat(current_key, suffix, i);
+
+ /* If all the letters in the suffix matched, then move to the
+ next trie. */
+ if(!suffix[i]) {
+ _get_approximate_trie(transition->next, &key[i], k, callback, data,
+ mismatches, current_key, max_key);
+ }
+ /* Otherwise, try out different kinds of mismatches. */
+ else if(k) {
+ int new_keylen = prev_keylen+i;
+
+ /* Letter replacement, skip the next letter in both the key and
+ suffix. */
+ if((new_keylen+1 < max_key) && key[i] && suffix[i]) {
+ current_key[new_keylen] = suffix[i];
+ current_key[new_keylen+1] = 0;
+ _get_approximate_transition(&key[i+1], k-1,
+ transition, &suffix[i+1],
+ callback, data,
+ mismatches+1, current_key, max_key);
+ current_key[new_keylen] = 0;
+ }
+
+ /* Insertion in key, skip the next letter in the key. */
+ if(key[i]) {
+ _get_approximate_transition(&key[i+1], k-1,
+ transition, &suffix[i],
+ callback, data,
+ mismatches+1, current_key, max_key);
+ }
+
+ /* Deletion from key, skip the next letter in the suffix. */
+ if((new_keylen+1 < max_key) && suffix[i]) {
+ current_key[new_keylen] = suffix[i];
+ current_key[new_keylen+1] = 0;
+ _get_approximate_transition(&key[i], k-1,
+ transition, &suffix[i+1],
+ callback, data,
+ mismatches+1, current_key, max_key);
+ current_key[new_keylen] = 0;
+ }
+ }
+ current_key[prev_keylen] = 0;
+}
+
+void
+_get_approximate_trie(const Trie trie, const unsigned char *key, const int k,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ const int mismatches,
+ void *data),
+ void *data,
+ const int mismatches,
+ unsigned char *current_key, const int max_key
+ )
+{
+ int i;
+
+ /* If there's no more key to match, then I'm done. */
+ if(!key[0]) {
+ if(trie->value)
+ (*callback)(current_key, trie->value, mismatches, data);
+ }
+ /* If there are no more mismatches allowed, then fall back to the
+ faster Trie_get. */
+ else if(!k) {
+ void *value = Trie_get(trie, key);
+ if(value) {
+ int l = strlen(current_key);
+ /* Make sure I have enough space for the full key. */
+ if(l + strlen(key) < max_key) {
+ strcat(current_key, key);
+ (*callback)(current_key, value, mismatches, data);
+ current_key[l] = 0;
+ }
+ /* BUG: Ran out of space for the key. This fails
+ silently, but should signal an error. */
+ }
+ }
+ /* If there are no more transitions, then all the characters left
+ in the key are mismatches. */
+ else if(!trie->num_transitions) {
+ if(trie->value && (strlen(key) <= k)) {
+ (*callback)(current_key, trie->value,
+ mismatches+strlen(key), data);
+ }
+ }
+ /* Otherwise, try to match each of the transitions. */
+ else {
+ for(i=0; i<trie->num_transitions; i++) {
+ Transition transition = &trie->transitions[i];
+ unsigned char *suffix = transition->suffix;
+ _get_approximate_transition(key, k, transition, suffix,
+ callback, data,
+ mismatches, current_key, max_key);
+ }
+ }
+
+}
+
+
+void
+Trie_get_approximate(const Trie trie, const unsigned char *key, const int k,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ const int mismatches,
+ void *data),
+ void *data
+ )
+{
+ KEY[0] = 0;
+ _get_approximate_trie(trie, key, k, callback, data, 0, KEY,MAX_KEY_LENGTH);
+}
+
+int Trie_len(const Trie trie)
+{
+ int i;
+ int length = 0;
+
+ if(!trie)
+ return 0;
+ if(trie->value)
+ length += 1;
+ for(i=0; i<trie->num_transitions; i++) {
+ length += Trie_len(trie->transitions[i].next);
+ }
+ return length;
+}
+
+int Trie_has_key(const Trie trie, const unsigned char *key)
+{
+ return Trie_get(trie, key) != NULL;
+}
+
+int Trie_has_prefix(const Trie trie, const unsigned char *prefix)
+{
+ int first, last, mid;
+
+ if(!prefix[0]) {
+ return 1;
+ }
+
+ /* The transitions are stored in alphabetical order. Do a binary
+ * search to find the proper one.
+ */
+ first = 0;
+ last = trie->num_transitions-1;
+ while(first <= last) {
+ Transition transition;
+ unsigned char *suffix;
+ int suffixlen, prefixlen, minlen;
+ int c;
+ mid = (first+last)/2;
+ transition = &trie->transitions[mid];
+ suffix = transition->suffix;
+ suffixlen = strlen(suffix);
+ prefixlen = strlen(prefix);
+ minlen = (suffixlen < prefixlen) ? suffixlen : prefixlen;
+ c = strncmp(prefix, suffix, minlen);
+ if(c < 0)
+ last = mid-1;
+ else if(c > 0)
+ first = mid+1;
+ else
+ return Trie_has_prefix(transition->next, prefix+minlen);
+ }
+ return 0;
+}
+
+static void
+_iterate_helper(const Trie trie,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data,
+ unsigned char *current_key, const int max_key)
+{
+ int i;
+ if(trie->value)
+ (*callback)(current_key, trie->value, data);
+ for(i=0; i<trie->num_transitions; i++) {
+ Transition transition = &trie->transitions[i];
+ unsigned char *suffix = transition->suffix;
+ int keylen = strlen(current_key);
+
+ if(keylen + strlen(suffix) >= max_key) {
+ /* BUG: This will fail silently. It should raise some
+ sort of error. */
+ continue;
+ }
+ strcat(current_key, suffix);
+ _iterate_helper(transition->next, callback, data,
+ current_key, max_key);
+ current_key[keylen] = 0;
+ }
+}
+
+void
+Trie_iterate(const Trie trie,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data)
+{
+ KEY[0] = 0;
+ _iterate_helper(trie, callback, data, KEY, MAX_KEY_LENGTH);
+}
+
+static void
+_with_prefix_helper(const Trie trie, const unsigned char *prefix,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data,
+ unsigned char *current_key, const int max_key)
+{
+ int first, last, mid;
+
+ if(!prefix[0]) {
+ _iterate_helper(trie, callback, data, current_key, max_key);
+ return;
+ }
+
+ /* The transitions are stored in alphabetical order. Do a binary
+ * search to find the proper one.
+ */
+ first = 0;
+ last = trie->num_transitions-1;
+ while(first <= last) {
+ Transition transition;
+ unsigned char *suffix;
+ int suffixlen, prefixlen, minlen;
+ int c;
+ mid = (first+last)/2;
+ transition = &trie->transitions[mid];
+ suffix = transition->suffix;
+ suffixlen = strlen(suffix);
+ prefixlen = strlen(prefix);
+ minlen = (suffixlen < prefixlen) ? suffixlen : prefixlen;
+ c = strncmp(prefix, suffix, minlen);
+ if(c < 0)
+ last = mid-1;
+ else if(c > 0)
+ first = mid+1;
+ else {
+ int keylen = strlen(current_key);
+ if(keylen + minlen >= max_key) {
+ /* BUG: This will fail silently. It should raise some
+ sort of error. */
+ break;
+ }
+ strncat(current_key, suffix, minlen);
+ _with_prefix_helper(transition->next, prefix+minlen,
+ callback, data, current_key, max_key);
+ current_key[keylen] = 0;
+ break;
+ }
+ }
+}
+
+void
+Trie_with_prefix(const Trie trie, const unsigned char *prefix,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data
+ )
+{
+ KEY[0] = 0;
+ _with_prefix_helper(trie, prefix, callback, data, KEY, MAX_KEY_LENGTH);
+}
+
+
+
+/* Need to declare _serialize_transition here so it can be called from
+ _serialize_trie. */
+int _serialize_transition(const Transition transition,
+ int (*write)(const void *towrite, const int length,
+ void *data),
+ int (*write_value)(const void *value, void *data),
+ void *data);
+
+/* This library also provides code for flattening tries so that they
+ * can be saved and read back in later. The format of a serialized
+ * trie is:
+ * TYPE NBYTES DESCRIPTION
+ * byte 1 Whether or not there is a value
+ * variable variable If there is a value, let the client store it.
+ * byte 1 Number of transitions for this Trie.
+ * transition variable
+ * int 4 Number of characters in the suffix.
+ * suffix variable the suffix for this transition
+ * byte 1 Whether or not there is a trie
+ * trie variable Recursively points to another trie.
+ *
+ * The number of bytes and the endian may vary from platform to
+ * platform.
+ */
+
+int _serialize_trie(const Trie trie,
+ int (*write)(const void *towrite, const int length,
+ void *data),
+ int (*write_value)(const void *value, void *data),
+ void *data)
+{
+ int i;
+ unsigned char has_value;
+
+ has_value = (trie->value != NULL);
+ if(!(*write)(&has_value, sizeof(has_value), data))
+ return 0;
+ if(has_value) {
+ if(!(*write_value)(trie->value, data))
+ return 0;
+ }
+
+ if(!(*write)(&trie->num_transitions, sizeof(trie->num_transitions), data))
+ return 0;
+ for(i=0; i<trie->num_transitions; i++) {
+ if(!_serialize_transition(&trie->transitions[i],
+ write, write_value, data))
+ return 0;
+ }
+
+ return 1;
+}
+
+int _serialize_transition(const Transition transition,
+ int (*write)(const void *towrite, const int length,
+ void *data),
+ int (*write_value)(const void *value, void *data),
+ void *data)
+{
+ int suffixlen;
+ unsigned char has_trie;
+
+ suffixlen = strlen(transition->suffix);
+ if(!(*write)(&suffixlen, sizeof(suffixlen), data))
+ return 0;
+ if(!(*write)(transition->suffix, suffixlen, data))
+ return 0;
+
+ has_trie = (transition->next != NULL);
+ if(!(*write)(&has_trie, sizeof(has_trie), data))
+ return 0;
+ if(has_trie) {
+ if(!_serialize_trie(transition->next, write, write_value, data))
+ return 0;
+ }
+ return 1;
+}
+
+int Trie_serialize(const Trie trie,
+ int (*write)(const void *towrite, const int length,
+ void *data),
+ int (*write_value)(const void *value, void *data),
+ void *data)
+{
+ int success = _serialize_trie(trie, write, write_value, data);
+ (*write)(NULL, 0, data);
+ return success;
+}
+
+int _deserialize_transition(Transition transition,
+ int (*read)(void *wasread, const int length,
+ void *data),
+ void *(*read_value)(void *data),
+ void *data);
+
+int _deserialize_trie(Trie trie,
+ int (*read)(void *wasread, const int length, void *data),
+ void *(*read_value)(void *data),
+ void *data)
+{
+ int i;
+ unsigned char has_value;
+
+ if(!(*read)(&has_value, sizeof(has_value), data))
+ goto _deserialize_trie_error;
+ if(has_value != 0 && has_value != 1)
+ goto _deserialize_trie_error;
+ if(has_value) {
+ if(!(trie->value = (*read_value)(data)))
+ goto _deserialize_trie_error;
+ }
+ if(!(*read)(&trie->num_transitions, sizeof(trie->num_transitions), data))
+ goto _deserialize_trie_error;
+ if(!(trie->transitions =
+ malloc(trie->num_transitions*sizeof(struct _Transition))))
+ goto _deserialize_trie_error;
+ for(i=0; i<trie->num_transitions; i++) {
+ if(!_deserialize_transition(&trie->transitions[i],
+ read, read_value, data))
+ goto _deserialize_trie_error;
+ }
+ return 1;
+
+ _deserialize_trie_error:
+ trie->num_transitions = 0;
+ if(trie->transitions) {
+ free(trie->transitions);
+ trie->transitions = NULL;
+ }
+ trie->value = NULL;
+ return 0;
+}
+
+int _deserialize_transition(Transition transition,
+ int (*read)(void *wasread, const int length,
+ void *data),
+ void *(*read_value)(void *data),
+ void *data)
+{
+ int suffixlen;
+ unsigned char has_trie;
+
+ if(!(*read)(&suffixlen, sizeof(suffixlen), data))
+ goto _deserialize_transition_error;
+ if(suffixlen < 0 || suffixlen >= MAX_KEY_LENGTH)
+ goto _deserialize_transition_error;
+ if(!(*read)(KEY, suffixlen, data))
+ goto _deserialize_transition_error;
+ KEY[suffixlen] = 0;
+ if(!(transition->suffix = (unsigned char *)strdup(KEY)))
+ goto _deserialize_transition_error;
+ if(!(*read)(&has_trie, sizeof(has_trie), data))
+ goto _deserialize_transition_error;
+ if(has_trie != 0 && has_trie != 1)
+ goto _deserialize_transition_error;
+ if(has_trie) {
+ transition->next = Trie_new();
+ if(!_deserialize_trie(transition->next, read, read_value, data))
+ goto _deserialize_transition_error;
+ }
+ return 1;
+
+ _deserialize_transition_error:
+ if(transition->suffix) {
+ free(transition->suffix);
+ transition->suffix = NULL;
+ }
+ if(transition->next) {
+ Trie_del(transition->next);
+ transition->next = NULL;
+ }
+ return 0;
+}
+
+Trie Trie_deserialize(int (*read)(void *wasread, const int length, void *data),
+ void *(*read_value)(void *data),
+ void *data)
+{
+ Trie trie = Trie_new();
+ if(!_deserialize_trie(trie, read, read_value, data)) {
+ Trie_del(trie);
+ return NULL;
+ }
+ return trie;
+}
+
+void test(void) {
+ Trie trie;
+
+ printf("Hello world!\n");
+
+ trie = Trie_new();
+ printf("New trie %p\n", trie);
+ Trie_set(trie, "hello world", "s1");
+ Trie_set(trie, "bye", "s2");
+ Trie_set(trie, "hell sucks", "s3");
+ Trie_set(trie, "hebee", "s4");
+
+ printf("%s\n", (char *)Trie_get(trie, "hello world"));
+ printf("%s\n", (char *)Trie_get(trie, "bye"));
+ printf("%s\n", (char *)Trie_get(trie, "hell sucks"));
+ printf("%s\n", (char *)Trie_get(trie, "hebee"));
+
+ Trie_set(trie, "blah", "s5");
+ printf("%s\n", (char *)Trie_get(trie, "blah"));
+
+ printf("%p\n", Trie_get(trie, "foobar"));
+ printf("%d\n", Trie_len(trie));
+
+ Trie_set(trie, "blah", "snew");
+ printf("%s\n", (char *)Trie_get(trie, "blah"));
+
+ Trie_del(trie);
+}
+
+#if 0
+int main() {
+ test();
+}
+#endif
--- /dev/null
+typedef struct _Trie *Trie;
+
+
+
+/* Trie_new
+ * --------
+ * Create a new trie. Return a Trie structure, which is an abstract
+ * data structure. The client should not have to know about the
+ * details of this structure. When finished, each Trie should be
+ * freed with Trie_del.
+ */
+Trie Trie_new(void);
+
+
+/* Trie_del
+ * --------
+ * Free a Trie data structure.
+ */
+void Trie_del(Trie trie);
+
+
+/* Trie_set
+ * --------
+ * Set a string in the Trie to some value. Returns a 0 if the
+ * function succeeded.
+ */
+int Trie_set(Trie trie, const unsigned char *key, const void *value);
+
+/* Trie_get
+ * --------
+ * Lookup whether a key exists in the Trie. Returns the value that
+ * was previous set in the Trie, or NULL if it doesn't exist.
+ */
+void *Trie_get(const Trie trie, const unsigned char *key);
+
+
+/* Trie_get_approximate
+ * --------------------
+ * Lookup whether a key exists in the Trie, allowing for mismatches to
+ * the dictionary. Passes back values using a callback function.
+ */
+void
+Trie_get_approximate(const Trie trie, const unsigned char *key, const int k,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ const int mismatches,
+ void *data),
+ void *data
+ );
+
+/* Trie_len
+ * --------
+ * Return the number of strings in the trie.
+ */
+int Trie_len(const Trie trie);
+
+
+/* Trie_has_key
+ * ------------
+ * Return whether a key exists in the trie.
+ */
+int Trie_has_key(const Trie trie, const unsigned char *key);
+
+
+/* Trie_has_prefix
+ * ---------------
+ * Return whether a string is a prefix of a key in the trie.
+ */
+int Trie_has_prefix(const Trie trie, const unsigned char *prefix);
+
+
+/* Trie_with_prefix
+ * ----------------
+ * Iterate over all the keys in the trie that start with a prefix.
+ */
+void Trie_with_prefix(const Trie trie, const unsigned char *prefix,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data
+ );
+
+
+/* Trie_iterate
+ * ------------
+ * Iterate through everything stored in the trie. callback is a
+ * function that gets called for each thing in the trie. It is called
+ * in arbitrary order. data is a pointer to some arbitrary data and
+ * gets passed unchanged to the callback.
+ */
+void Trie_iterate(const Trie trie,
+ void (*callback)(const unsigned char *key,
+ const void *value,
+ void *data),
+ void *data
+ );
+
+/* Trie_serialize
+ * --------------
+ * Serialize a tree into a stream of bytes. This function takes a
+ * callback 'write' that should take a pointer to data and the length
+ * of the data in bytes. This will be called repeatedly until the
+ * whole Trie is serialized. When it is done, this function will call
+ * 'write' with a length of 0. Since the values are handled by the
+ * client, this function also takes a callback function 'write_value'
+ * so that the client can serialize their own values.
+ *
+ * This function is platform-dependent, so byte streams created on one
+ * machine may not necessarily port to another.
+ */
+int Trie_serialize(const Trie trie,
+ int (*write)(const void *towrite, const int length,
+ void *data),
+ int (*write_value)(const void *value, void *data),
+ void *data);
+
+
+
+/* Trie_deserialize
+ * ----------------
+ * Deserialize a tree that was previously serialized with
+ * Trie_serialize. This function takes a callback 'read' that should
+ * read 'length' bytes and save it to 'wasread'. 'read_value' should
+ * read a value and return a pointer to it. 'data' is a pointer that
+ * will be passed unchanged to 'read' and 'read_value'.
+ */
+Trie Trie_deserialize(int (*read)(void *wasread, const int length, void *data),
+ void *(*read_value)(void *data),
+ void *data);
--- /dev/null
+"""
+Given a trie, find all occurrences of a word in the trie in a string.
+
+Like searching a string for a substring, except that the substring is
+any word in a trie.
+
+Functions:
+match Find longest key in a trie matching the beginning of the string.
+match_all Find all keys in a trie matching the beginning of the string.
+find Find keys in a trie matching anywhere in a string.
+find_words Find keys in a trie matching whole words in a string.
+
+"""
+import string
+import re
+
+def match(string, trie):
+ """match(string, trie) -> longest key or None
+
+ Find the longest key in the trie that matches the beginning of the
+ string.
+
+ """
+ longest = None
+ for i in range(len(string)):
+ substr = string[:i+1]
+ if not trie.has_prefix(substr):
+ break
+ if trie.has_key(substr):
+ longest = substr
+ return longest
+
+def match_all(string, trie):
+ """match_all(string, trie) -> list of keys
+
+ Find all the keys in the trie that matches the beginning of the
+ string.
+
+ """
+ matches = []
+ for i in range(len(string)):
+ substr = string[:i+1]
+ if not trie.has_prefix(substr):
+ break
+ if trie.has_key(substr):
+ matches.append(substr)
+ return matches
+
+def find(string, trie):
+ """find(string, trie) -> list of tuples (key, start, end)
+
+ Find all the keys in the trie that match anywhere in the string.
+
+ """
+ results = []
+ start = 0 # index to start the search
+ while start < len(string):
+ # Look for a match.
+ keys = match_all(string[start:], trie)
+ for key in keys:
+ results.append((key, start, start+len(key)))
+ start += 1
+ return results
+
+DEFAULT_BOUNDARY_CHARS = string.punctuation + string.whitespace
+
+def find_words(string, trie):
+ """find_words(string, trie) -> list of tuples (key, start, end)
+
+ Find all the keys in the trie that match full words in the string.
+ Word boundaries are defined as any punctuation or whitespace.
+
+ """
+ _boundary_re = re.compile(r"[%s]+" % re.escape(DEFAULT_BOUNDARY_CHARS))
+
+ results = []
+ start = 0 # index of word boundary
+ while start < len(string):
+ # Look for a match.
+ keys = match_all(string[start:], trie)
+ for key in keys:
+ l = len(key)
+ # Make sure it ends at a boundary.
+ if start+l == len(string) or \
+ _boundary_re.match(string[start+l]):
+ results.append((key, start, start+l))
+ # Move forward to the next boundary.
+ m = _boundary_re.search(string, start)
+ if m is None:
+ break
+ start = m.end()
+ return results
--- /dev/null
+#include <Python.h>
+#include <marshal.h>
+#include "trie.h"
+
+#if PY_VERSION_HEX < 0x02050000
+#define Py_ssize_t int
+#endif
+
+
+
+staticforward PyTypeObject Trie_Type;
+
+typedef struct {
+ PyObject_HEAD
+ Trie trie;
+} trieobject;
+
+static PyObject*
+trie_trie(PyObject* self, PyObject* args)
+{
+ trieobject* trieobj;
+ Trie trie;
+
+ if (!PyArg_ParseTuple(args,":trie"))
+ return NULL;
+ if(!(trie = Trie_new()))
+ return PyErr_NoMemory();
+ if(!(trieobj = PyObject_New(trieobject, &Trie_Type)))
+ return NULL;
+ trieobj->trie = trie;
+ return (PyObject*)trieobj;
+}
+
+static void
+_decref_objects(const unsigned char *key, const void *value, void *data)
+{
+ Py_DECREF((PyObject *)value);
+}
+
+static void
+trie_dealloc(PyObject* self)
+{
+ trieobject *mp = (trieobject *)self;
+ Trie_iterate(mp->trie, _decref_objects, NULL);
+ Trie_del(mp->trie);
+ PyObject_Del(self);
+}
+
+static Py_ssize_t
+trie_length(trieobject *mp)
+{
+ return Trie_len(mp->trie);
+}
+
+static PyObject *
+trie_subscript(trieobject *mp, PyObject *py_key)
+{
+ unsigned char *key;
+ PyObject *py_value;
+
+ /* Make sure key is a string. */
+ if(!PyString_Check(py_key)) {
+ PyErr_SetString(PyExc_TypeError, "key must be a string");
+ return NULL;
+ }
+ key = (unsigned char *)PyString_AS_STRING(py_key);
+ py_value = (PyObject *)Trie_get(mp->trie, key);
+ if(py_value == NULL)
+ PyErr_SetString(PyExc_KeyError, (char *)key);
+ else
+ Py_INCREF(py_value);
+ return py_value;
+}
+
+static int
+trie_ass_sub(trieobject *mp, PyObject *py_key, PyObject *py_value)
+{
+ unsigned char *key;
+ PyObject *py_prev;
+
+ /* Make sure key is a string. */
+ if(!PyString_Check(py_key)) {
+ PyErr_SetString(PyExc_TypeError, "key must be a string");
+ return -1;
+ }
+ key = (unsigned char *)PyString_AS_STRING((char *)py_key);
+
+ /* Check to see whether something already exists at that key. If
+ there's already an object there, then I will have to remove it.
+ */
+ py_prev = (PyObject *)Trie_get(mp->trie, key);
+ if(py_prev) {
+ Py_DECREF(py_prev);
+ }
+
+ /* The client wants to delete a key from a dictionary. The Trie
+ API doesn't support this, so I will just overwrite it with
+ NULL. */
+ if(!py_value) {
+ /* If the key doesn't exist, raise a KeyError. */
+ if(!py_prev) {
+ PyErr_SetString(PyExc_KeyError, (char *)key);
+ return -1;
+ }
+ Trie_set(mp->trie, key, NULL);
+ }
+ /* The client wants to set a key in the dictionary. */
+ else {
+ Py_INCREF(py_value);
+ if(Trie_set(mp->trie, key, py_value)) {
+ PyErr_SetString(PyExc_AssertionError, "error setting trie");
+ return -1;
+ }
+ }
+ return 0;
+}
+
+static char has_key__doc__[] =
+"D.has_key(k) -> 1 if D has a key k, else 0";
+
+static PyObject *
+trie_has_key(trieobject *mp, PyObject *py_key)
+{
+ unsigned char *key;
+ int has_key;
+
+ /* Make sure key is a string. */
+ if(!PyString_Check(py_key)) {
+ PyErr_SetString(PyExc_TypeError, "key must be a string");
+ return NULL;
+ }
+ key = (unsigned char *)PyString_AS_STRING(py_key);
+ has_key = Trie_has_key(mp->trie, key);
+ return PyInt_FromLong((long)has_key);
+}
+
+static PyObject *
+trie_has_key_onearg(trieobject *mp, PyObject *py_args)
+{
+ PyObject *py_arg;
+ if(!PyArg_ParseTuple(py_args, "O", &py_arg))
+ return NULL;
+ return trie_has_key(mp, py_arg);
+}
+
+
+
+static char has_prefix__doc__[] =
+"D.has_prefix(k) -> 1 if D has a prefix k, else 0";
+
+static PyObject *
+trie_has_prefix(trieobject *mp, PyObject *py_prefix)
+{
+ unsigned char *prefix;
+ int has_prefix;
+
+ /* Make sure prefix is a string. */
+ if(!PyString_Check(py_prefix)) {
+ PyErr_SetString(PyExc_TypeError, "k must be a string");
+ return NULL;
+ }
+ prefix = (unsigned char *)PyString_AS_STRING(py_prefix);
+ has_prefix = Trie_has_prefix(mp->trie, prefix);
+ return PyInt_FromLong((long)has_prefix);
+}
+
+static PyObject *
+trie_has_prefix_onearg(trieobject *mp, PyObject *py_args)
+{
+ PyObject *py_arg;
+ if(!PyArg_ParseTuple(py_args, "O", &py_arg))
+ return NULL;
+ return trie_has_prefix(mp, py_arg);
+}
+
+static char with_prefix__doc__[] =
+"D.with_prefix(prefix) -> list of D's keys that begins with prefix";
+
+static void
+_trie_with_prefix_helper(const unsigned char *key, const void *value,
+ void *data)
+{
+ PyObject *py_list = (PyObject *)data;
+ PyObject *py_key;
+
+ if(PyErr_Occurred())
+ return;
+
+ if(!(py_key = PyString_FromString((const char *)key)))
+ return;
+ PyList_Append(py_list, py_key);
+ Py_DECREF(py_key);
+}
+
+static PyObject *
+trie_with_prefix(trieobject *mp, PyObject *py_prefix)
+{
+ unsigned char *prefix;
+ PyObject *py_list;
+
+ /* Make sure prefix is a string. */
+ if(!PyString_Check(py_prefix)) {
+ PyErr_SetString(PyExc_TypeError, "k must be a string");
+ return NULL;
+ }
+ prefix = (unsigned char *)PyString_AS_STRING(py_prefix);
+
+ if(!(py_list = PyList_New(0)))
+ return NULL;
+ Trie_with_prefix(mp->trie, prefix,
+ _trie_with_prefix_helper, (void *)py_list);
+ if(PyErr_Occurred()) {
+ Py_DECREF(py_list);
+ return NULL;
+ }
+ return py_list;
+}
+
+static PyObject *
+trie_with_prefix_onearg(trieobject *mp, PyObject *py_args)
+{
+ PyObject *py_arg;
+ if(!PyArg_ParseTuple(py_args, "O", &py_arg))
+ return NULL;
+ return trie_with_prefix(mp, py_arg);
+}
+
+
+static char keys__doc__[] =
+"D.keys() -> list of D's keys";
+
+static void
+_trie_keys_helper(const unsigned char *key, const void *value, void *data)
+{
+ PyObject *py_list = (PyObject *)data;
+ PyObject *py_key;
+
+ if(PyErr_Occurred())
+ return;
+
+ if(!(py_key = PyString_FromString((char *)key)))
+ return;
+ PyList_Append(py_list, py_key);
+ Py_DECREF(py_key);
+}
+
+static PyObject *
+trie_keys(trieobject *mp)
+{
+ PyObject *py_list;
+
+ if(!(py_list = PyList_New(0)))
+ return NULL;
+ Trie_iterate(mp->trie, _trie_keys_helper, (void *)py_list);
+ if(PyErr_Occurred()) {
+ Py_DECREF(py_list);
+ return NULL;
+ }
+ return py_list;
+}
+
+static PyObject *
+trie_keys_noargs(trieobject *mp, PyObject *py_args)
+{
+ if(PyTuple_Size(py_args) != 0) {
+ PyErr_SetString(PyExc_ValueError, "no args expected");
+ return NULL;
+ }
+ return trie_keys(mp);
+}
+
+static char values__doc__[] =
+"D.values() -> list of D's values";
+
+static void
+_trie_values_helper(const unsigned char *key, const void *value, void *data)
+{
+ PyObject *py_list = (PyObject *)data;
+ if(PyErr_Occurred())
+ return;
+ PyList_Append(py_list, (PyObject *)value);
+}
+
+static PyObject *
+trie_values(trieobject *mp)
+{
+ PyObject *py_list;
+
+ if(!(py_list = PyList_New(0)))
+ return NULL;
+ Trie_iterate(mp->trie, _trie_values_helper, (void *)py_list);
+ if(PyErr_Occurred()) {
+ Py_DECREF(py_list);
+ return NULL;
+ }
+ return py_list;
+}
+
+static PyObject *
+trie_values_noargs(trieobject *mp, PyObject *py_args)
+{
+ if(PyTuple_Size(py_args) != 0) {
+ PyErr_SetString(PyExc_ValueError, "no args expected");
+ return NULL;
+ }
+ return trie_values(mp);
+}
+
+static char get__doc__[] =
+"D.get(k[,d]) -> D[k] if D.has_key(k), else d. d defaults to None.";
+
+static PyObject *
+trie_get(trieobject *mp, PyObject *args)
+{
+ unsigned char *key;
+ PyObject *py_value;
+ PyObject *py_failobj = Py_None;
+
+ if (!PyArg_ParseTuple(args, "s|O:get", &key, &py_failobj))
+ return NULL;
+ py_value = (PyObject *)Trie_get(mp->trie, key);
+ if(!py_value)
+ py_value = py_failobj;
+ Py_INCREF(py_value);
+ return py_value;
+}
+
+static char get_approximate__doc__[] =
+"D.get_approximate(key, k) -> List of (key, value, mismatches) in D, allowing up to k mismatches in key.";
+
+void
+_trie_get_approximate_helper(const unsigned char *key, const void *value,
+ const int mismatches, void *data)
+{
+ /* Append a tuple of (key, value) to data, which is a PyList. */
+ PyObject *py_list = (PyObject *)data,
+ *py_value = (PyObject *)value,
+ *py_key,
+ *py_tuple,
+ *py_mismatches;
+
+ if(PyErr_Occurred())
+ return;
+
+ if(!(py_key = PyString_FromString((const char *)key)))
+ return;
+ if(!(py_mismatches = PyInt_FromLong(mismatches))) {
+ Py_DECREF(py_key);
+ return;
+ }
+ Py_INCREF(py_value);
+
+ if(!(py_tuple = PyTuple_New(3))) {
+ Py_DECREF(py_key);
+ Py_DECREF(py_mismatches);
+ Py_DECREF(py_value);
+ return;
+ }
+ PyTuple_SetItem(py_tuple, 0, py_key);
+ PyTuple_SetItem(py_tuple, 1, py_value);
+ PyTuple_SetItem(py_tuple, 2, py_mismatches);
+ PyList_Append(py_list, py_tuple);
+ Py_DECREF(py_tuple);
+}
+
+static PyObject *
+trie_get_approximate(trieobject *mp, PyObject *args)
+{
+ unsigned char *key;
+ int k;
+ PyObject *py_list;
+
+ if (!PyArg_ParseTuple(args, "si:get_approximate", &key, &k))
+ return NULL;
+
+ if(!(py_list = PyList_New(0)))
+ return NULL;
+ Trie_get_approximate(mp->trie, key, k,
+ _trie_get_approximate_helper, (void *)py_list);
+ if(PyErr_Occurred()) {
+ Py_DECREF(py_list);
+ return NULL;
+ }
+ return py_list;
+}
+
+static long
+trie_nohash(PyObject *self)
+{
+ PyErr_SetString(PyExc_TypeError, "trie objects are unhashable");
+ return -1;
+}
+
+static PyMappingMethods trie_as_mapping = {
+/* The first member of PyMappingMethods was redefined in Python 2.5. */
+#if PY_VERSION_HEX < 0x02050000
+ (inquiry)trie_length, /*mp_length*/
+#else
+ (lenfunc)trie_length, /*mp_length*/
+#endif
+ (binaryfunc)trie_subscript, /*mp_subscript*/
+ (objobjargproc)trie_ass_sub /*mp_ass_subscript*/
+};
+
+static PyMethodDef trieobj_methods[] = {
+ /* METH_O and METH_NOARGS require Python 2.2.
+ {"has_key", (PyCFunction)trie_has_key, METH_O,
+ has_key__doc__},
+ {"has_prefix", (PyCFunction)trie_has_prefix, METH_O,
+ has_prefix__doc__},
+ {"with_prefix", (PyCFunction)trie_with_prefix, METH_O,
+ with_prefix__doc__},
+ {"keys", (PyCFunction)trie_keys, METH_NOARGS,
+ keys__doc__},
+ {"values", (PyCFunction)trie_values, METH_NOARGS,
+ values__doc__},
+ */
+
+ {"has_key", (PyCFunction)trie_has_key_onearg, METH_VARARGS,
+ has_key__doc__},
+ {"has_prefix", (PyCFunction)trie_has_prefix_onearg, METH_VARARGS,
+ has_prefix__doc__},
+ {"with_prefix", (PyCFunction)trie_with_prefix_onearg, METH_VARARGS,
+ with_prefix__doc__},
+ {"keys", (PyCFunction)trie_keys_noargs, METH_VARARGS,
+ keys__doc__},
+ {"values", (PyCFunction)trie_values_noargs, METH_VARARGS,
+ values__doc__},
+
+ {"get", (PyCFunction)trie_get, METH_VARARGS,
+ get__doc__},
+ {"get_approximate", (PyCFunction)trie_get_approximate, METH_VARARGS,
+ get_approximate__doc__},
+ {NULL, NULL} /* sentinel */
+};
+
+static PyObject *trie_getattr(PyObject *obj, char *name)
+{
+ return Py_FindMethod(trieobj_methods, (PyObject *)obj, name);
+
+}
+
+static PyTypeObject Trie_Type = {
+ PyObject_HEAD_INIT(NULL)
+ 0,
+ "trie",
+ sizeof(trieobject),
+ 0,
+ trie_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ trie_getattr, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ &trie_as_mapping, /*tp_as_mapping*/
+ trie_nohash, /*tp_hash */
+};
+
+static int
+_write_to_handle(const void *towrite, const int length, void *handle)
+{
+ PyObject *py_handle = (PyObject *)handle,
+ *py_retval = NULL;
+ int success = 0;
+
+ if(!length)
+ return 1;
+
+ if(!(py_retval = PyObject_CallMethod(py_handle, "write", "s#",
+ towrite, length)))
+ goto _write_to_handle_cleanup;
+ success = 1;
+
+ _write_to_handle_cleanup:
+ if(py_retval) {
+ Py_DECREF(py_retval);
+ }
+ return success;
+}
+
+int _write_value_to_handle(const void *value, void *handle)
+{
+ PyObject *py_value = (PyObject *)value,
+ *py_marshalled = NULL;
+ char *marshalled;
+ Py_ssize_t length;
+ int success = 0;
+
+#ifdef Py_MARSHAL_VERSION
+ if(!(py_marshalled =
+ PyMarshal_WriteObjectToString(py_value, Py_MARSHAL_VERSION)))
+ goto _write_value_to_handle_cleanup;
+#else
+ if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value)))
+ goto _write_value_to_handle_cleanup;
+#endif
+ if(PyString_AsStringAndSize(py_marshalled, &marshalled, &length) == -1)
+ goto _write_value_to_handle_cleanup;
+ if(!_write_to_handle(&length, sizeof(length), handle))
+ goto _write_value_to_handle_cleanup;
+ if (length != (int)length)
+ goto _write_value_to_handle_cleanup;
+ if(!_write_to_handle(marshalled, (int)length, handle))
+ goto _write_value_to_handle_cleanup;
+ success = 1;
+
+ _write_value_to_handle_cleanup:
+ if(py_marshalled) {
+ Py_DECREF(py_marshalled);
+ }
+
+ return success;
+}
+
+static PyObject *
+trie_save(PyObject *self, PyObject *args)
+{
+ PyObject *py_handle,
+ *py_trie;
+ trieobject *mp;
+
+ if(!PyArg_ParseTuple(args, "OO:save", &py_handle, &py_trie))
+ return NULL;
+ mp = (trieobject *)py_trie;
+ if(!Trie_serialize(mp->trie, _write_to_handle, _write_value_to_handle,
+ (void *)py_handle)) {
+ if(!PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError,
+ "saving failed for some reason");
+ return NULL;
+ }
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+
+static int
+_read_from_handle(void *wasread, const int length, void *handle)
+{
+ PyObject *py_handle = (PyObject *)handle,
+ *py_retval = NULL;
+ void *retval;
+ int success = 0;
+ PyBufferProcs *buffer;
+ int segment;
+ int bytes_read, bytes_left;
+
+ if(!length)
+ return 1;
+
+ if(!(py_retval = PyObject_CallMethod(py_handle, "read", "i", length)))
+ goto _read_from_handle_cleanup;
+ if(!py_retval->ob_type->tp_as_buffer) {
+ PyErr_SetString(PyExc_ValueError, "read method should return buffer");
+ goto _read_from_handle_cleanup;
+ }
+ if(!(py_retval->ob_type->tp_flags & Py_TPFLAGS_DEFAULT)) {
+ PyErr_SetString(PyExc_ValueError, "no bf_getcharbuffer slot");
+ goto _read_from_handle_cleanup;
+ }
+ buffer = py_retval->ob_type->tp_as_buffer;
+ if(!buffer->bf_getreadbuffer) {
+ PyErr_SetString(PyExc_ValueError, "no bf_getreadbuffer");
+ goto _read_from_handle_cleanup;
+ }
+
+ bytes_left = length;
+ segment = 0;
+ while(bytes_left > 0) {
+ if((bytes_read = buffer->bf_getreadbuffer(py_retval,
+ segment, &retval)) == -1)
+ goto _read_from_handle_cleanup;
+ memcpy(wasread, retval, bytes_read);
+ wasread = (void *)((char *)wasread + bytes_read);
+ bytes_left -= bytes_read;
+ segment += 1;
+ }
+
+ success = 1;
+
+ _read_from_handle_cleanup:
+ if(py_retval) {
+ Py_DECREF(py_retval);
+ }
+ return success;
+}
+
+#define MAX_KEY_LENGTH 2000
+static void *
+_read_value_from_handle(void *handle)
+{
+ Py_ssize_t length;
+ char KEY[MAX_KEY_LENGTH];
+
+ if(!_read_from_handle((void *)&length, sizeof(length), (void *)handle))
+ return NULL;
+ if(length < 0 || length >= MAX_KEY_LENGTH)
+ return NULL;
+ if(!_read_from_handle((void *)KEY, length, (void *)handle))
+ return NULL;
+ return PyMarshal_ReadObjectFromString(KEY, length);
+}
+
+
+static PyObject *
+trie_load(PyObject *self, PyObject *args)
+{
+ PyObject *py_handle;
+ Trie trie;
+ trieobject *trieobj;
+
+ if(!PyArg_ParseTuple(args, "O:load", &py_handle))
+ return NULL;
+
+ if(!(trie = Trie_deserialize(_read_from_handle, _read_value_from_handle,
+ py_handle))) {
+ if(!PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError,
+ "loading failed for some reason");
+ return NULL;
+ }
+
+ if(!(trieobj = PyObject_New(trieobject, &Trie_Type))) {
+ Trie_del(trie);
+ return NULL;
+ }
+ trieobj->trie = trie;
+ return (PyObject *)trieobj;
+}
+
+static PyMethodDef trie_methods[] = {
+ {"trie", trie_trie, METH_VARARGS,
+ "trie() -> new Trie object."},
+ {"load", trie_load, METH_VARARGS,
+ "load(handle) -> trie object"},
+ {"save", trie_save, METH_VARARGS,
+ "save(handle, trie), save a trie object to a handle"},
+ {NULL, NULL, 0, NULL}
+};
+
+static char trie__doc__[] =
+"\
+This module implements a trie data structure. This allows an O(M)\n\
+lookup of a string in a dictionary, where M is the length of the\n\
+string. It also supports approximate matches.\n\
+\n\
+Functions:\n\
+trie Create a new trie object.\n\
+save Save a trie to a handle.\n\
+load Load a trie from a handle.\n\
+\n\
+";
+
+DL_EXPORT(void)
+inittrie(void)
+{
+ Trie_Type.ob_type = &PyType_Type;
+
+ (void) Py_InitModule3("trie", trie_methods, trie__doc__);
+}
--- /dev/null
+# Copyright 2000 by Andrew Dalke.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Miscellaneous functions for dealing with sequences (obsolete?)."""
+
+import Seq
+import Alphabet
+
+from PropertyManager import default_manager
+
+def translate(seq, id = None):
+ """Translate a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.translate() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the translate method or function in Bio.Seq"\
+ +" instead, as described in the Tutorial.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.translate(seq)
+
+def translate_to_stop(seq, id = None):
+ """Translate a sequence up to the first in frame stop codon (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.translate_to_stop() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the translate method or function in Bio.Seq"\
+ +" instead, as described in the Tutorial.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.translate_to_stop(seq)
+
+def back_translate(seq, id = None):
+ """Back-translate a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.back_translate() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" If you use it, please tell us on the mailing list.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.back_translate(seq)
+
+
+def transcribe(seq):
+ """Transcribe a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.transcribe() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the transcribe method or function in"\
+ +" Bio.Seq instead, as described in the Tutorial.",
+ DeprecationWarning)
+ transcriber = default_manager.resolve(seq.alphabet, "transcriber")
+ return transcriber.transcribe(seq)
+
+def back_transcribe(seq):
+ """Back-transcribe a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.back_transcribe() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the back_transcribe method or function in"\
+ +" Bio.Seq instead, as described in the Tutorial.",
+ DeprecationWarning)
+ transcriber = default_manager.resolve(seq.alphabet, "transcriber")
+ return transcriber.back_transcribe(seq)
+
+def ungap(seq):
+ """given a sequence with gap encoding, return the ungapped sequence"""
+ #TODO - Fix this? It currently assumes the outmost AlphabetEncoder
+ #is for the gap. Consider HasStopCodon(Gapped(Protein())) as a test case.
+ gap = seq.gap_char
+ letters = []
+ for c in seq.data:
+ if c != gap:
+ letters.append(c)
+ return Seq.Seq("".join(letters), seq.alphabet.alphabet)
+
+def verify_alphabet(seq):
+ letters = {}
+ for c in seq.alphabet.letters:
+ letters[c] = 1
+ try:
+ for c in seq.data:
+ letters[c]
+ except KeyError:
+ return 0
+ return 1
+
+def count_monomers(seq):
+ dict = {}
+# bugfix: string.count(s,c) raises an AttributeError. Iddo Friedberg 16 Mar. 04
+# s = buffer(seq.data) # works for strings and array.arrays
+ for c in seq.alphabet.letters:
+ dict[c] = seq.data.count(c)
+ return dict
+
+def percent_monomers(seq):
+ dict2 = {}
+ seq_len = len(seq)
+ dict = count_monomers(seq)
+ for m in dict:
+ dict2[m] = dict[m] * 100. / seq_len
+ return dict2
+
+def sum(seq, table, zero = 0.0):
+ total = zero
+ for c in getattr(seq, "data", seq):
+ total = total + table[c]
+ return total
+
+# For ranged addition
+def sum_2ple(seq, table, zero = (0.0, 0.0)):
+ x, y = zero
+ data = getattr(seq, "data", seq)
+ for c in data:
+ x2, y2 = table[c]
+ x = x + x2
+ y = y + y2
+ return (x, y)
+
+def total_weight(seq, weight_table = None):
+ if weight_table is None:
+ weight_table = default_manager.resolve(seq.alphabet, "weight_table")
+ return sum(seq, weight_table)
+
+def total_weight_range(seq, weight_table = None):
+ if weight_table is None:
+ weight_table = default_manager.resolve(seq.alphabet, "weight_range_table")
+ return sum_2ple(seq, weight_table)
+
+def reduce_sequence(seq, reduction_table,new_alphabet=None):
+ """ given an amino-acid sequence, return it in reduced alphabet form based
+ on the letter-translation table passed. Some "standard" tables are in
+ Alphabet.Reduced.
+ seq: a Seq.Seq type sequence
+ reduction_table: a dictionary whose keys are the "from" alphabet, and values
+ are the "to" alphabet"""
+ if new_alphabet is None:
+ new_alphabet = Alphabet.single_letter_alphabet
+ new_alphabet.letters = ''
+ for letter in reduction_table:
+ new_alphabet.letters += letter
+ new_alphabet.size = len(new_alphabet.letters)
+ new_seq = Seq.Seq('',new_alphabet)
+ for letter in seq:
+ new_seq += reduction_table[letter]
+ return new_seq
+
+
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+# This is a Python module.
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+# Not clear on the distinction, if any, between 'embl' and 'embl/65'. This
+# code might apply to either or both.
+
+# See 'http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html' for a
+# definition of this file format.
+
+# This code only makes a best effort--the output may not be strictly valid.
+# So, for example, the EMBL ID is supposed to be alphanumeric, starting with a
+# letter, but we don't check for this, etc.
+
+
+# Example:
+# ID AA03518 standard; DNA; FUN; 237 BP.
+# XX
+# AC U03518;
+# XX
+# DE Aspergillus awamori internal transcribed spacer 1 (ITS1) and 18S
+# DE rRNA and 5.8S rRNA genes, partial sequence.
+# XX
+# SQ Sequence 237 BP; 41 A; 77 C; 67 G; 52 T; 0 other;
+# aacctgcgga aggatcatta ccgagtgcgg gtcctttggg cccaacctcc catccgtgtc 60
+# tattgtaccc tgttgcttcg gcgggcccgc cgcttgtcgg ccgccggggg ggcgcctctg 120
+# ccccccgggc ccgtgcccgc cggagacccc aacacgaaca ctgtctgaaa gcgtgcagtc 180
+# tgagttgatt gaatgcaatc agttaaaact ttcaacaatg gatctcttgg ttccggc 237
+# //
+
+
+import textwrap
+
+from Bio import Alphabet
+from Bio import Writer
+
+class WriteEmbl(Writer.Writer):
+ def __init__(self, outfile):
+ Writer.Writer.__init__(self, outfile)
+
+ def write(self, record):
+ seq = record.seq
+ assert seq.alphabet.size == 1, "cannot handle alphabet of size %d" % \
+ seq.alphabet.size
+ data = seq.data
+ upperdata = data.upper()
+
+# It'd be nice if the alphabet was usefully set, but for many interesting
+# cases (e.g., reading from FASTA files), it's not.
+
+ if isinstance(seq.alphabet, Alphabet.RNAAlphabet):
+ molecule = 'mRNA'
+ letters = ['A', 'C', 'G', 'U']
+ else:
+ molecule = 'DNA'
+ letters = ['A', 'C', 'G', 'T']
+
+ division = 'UNC' # unknown
+
+ self.outfile.write("ID %s standard; %s; %s; %d BP.\n"
+ % (record.id, molecule, division, len(data)))
+
+ desclist = textwrap.wrap(record.description, 74)
+ for l in desclist:
+ self.outfile.write("DE %s\n" % l)
+
+ counts = [ upperdata.count(l) for l in letters ]
+ othercount = len(upperdata) - sum(counts)
+
+ countstring = ''.join([ " %d %s;" % p for p in zip(counts, letters) ])
+
+ self.outfile.write("SQ Sequence %s BP;%s %d other;\n"
+ % (len(data), countstring, othercount))
+
+ rowlength = 60
+ blocklength = 10
+ for i in xrange(0, len(data), rowlength):
+ self.outfile.write(" " * 5)
+ row = data[i:i+rowlength]
+ for b in xrange(0, rowlength, blocklength):
+ block = row[b:b+blocklength]
+ self.outfile.write("%-*s" % (blocklength+1, block))
+ self.outfile.write("%9d\n" % min(i+rowlength, len(data)))
+
+ self.outfile.write("//\n")
+
+
+make_writer = WriteEmbl
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+from Bio import Writer
+
+class WriteEmpty(Writer.Writer):
+ pass
+
+make_writer = WriteEmpty
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+from Bio import Writer
+
+class WriteFasta(Writer.Writer):
+ def __init__(self, outfile, seqwidth = 72):
+ Writer.Writer.__init__(self, outfile)
+ assert seqwidth > 0, seqwidth
+ self.seqwidth = seqwidth
+
+ def write(self, record):
+ self.outfile.write(">%s %s\n" % (record.id, record.description))
+ seq = record.seq
+ assert seq.alphabet.size == 1, "cannot handle alphabet of size %d" % \
+ seq.alphabet.size
+ seq = seq.data
+ seqwidth = self.seqwidth
+ for i in range(0, len(seq), seqwidth):
+ self.outfile.write(seq[i:i+seqwidth])
+ self.outfile.write("\n")
+
+make_writer = WriteFasta
--- /dev/null
+"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
+# This is a Python module.
+# (there are more files underneath this directory)
--- /dev/null
+CONTRIBUTORS
+============
+
+This is a list of people who have made contributions to Biopython.
+This is certainly not comprehensive, and if you've been overlooked
+(sorry!), please mention it on the development mailing list.
+
+Cecilia Alsmark <Cecilia.Alsmark at domain ebc.uu.se>
+Tiago Antao <tiagoantao at gmail.com>
+Sebastian Bassi <sbassi at domain asalup.org>
+Bill Barnard <bill at domain barnard-engineering.com>
+Yves Bastide <ybastide at domain irisa.fr>
+Yair Benita <Y.Benita at domain pharm.uu.nl>
+Peter Bienstman <Peter.Bienstman at domain rug.ac.be>
+Bob Bussell <rgb2003 at domain med.cornell.edu>
+Diego Brouard <diego at domain conysis.com>
+James Casbon <j.a.casbon at domain qmul.ac.uk>
+Hye-Shik Chang <perky at domain fallin.lv>
+Jeffrey Chang <jchang at domain smi.stanford.edu>
+Brad Chapman <chapmanb at domain arches.uga.edu>
+Peter Cock <p.j.a.cock at googlemail dot com>
+Marc Colosimo <mcolosimo at domain mitre.org>
+Cymon J Cox <cymon at domain duke.edu>
+Gavin E Crooks <gec at domain compbio.berkeley.edu>
+Andrew Dalke <dalke at domain acm.org>
+Michiel de Hoon <mdehoon at domain c2b2.columbia.edu>
+Sjoerd de Vries <sjoerd at domain nmr.chem.uu.nl>
+Iddo Friedberg <idoerg at domain burnham.org>
+Bertrand Frottier <bertrand.frottier at domain free.fr>
+Jason A. Hackney <jhackney at domain stanford.edu>
+Thomas Hamelryck <thamelry at domain binf.ku.dk>
+Michael Hoffman <hoffman+biopython at domain ebi.ac.uk>
+Yu Huang <krocea at domain yahoo.com.cn>
+Frank Kauff <fkauff at domain duke.edu>
+Andreas Kuntzagk <andreas.kuntzagk at domain mdc-berlin.de>
+Michal Kurowski <michal at domain genesilico.pl>
+Chris Lasher <chris.lasher at gmail.com>
+Gaetan Lehman <gaetan.lehmann at domain jouy.inra.fr>
+Katharine Lindner <katel at domain worldpath.net>
+Tarjei Mikkelsen <tarjei at domain genome.wi.mit.edu>
+Cheng Soon Ong <chengsoon.ong at tuebingen.mpg.de>
+Mike Poidinger <Michael.Poidinger at domain eBioinformatics.com>
+Leighton Pritchard <lpritc at domain scri.sari.ac.uk>
+Wolfgang Schueler <wolfgang at domain proceryon.at>
+Peter Slickers <piet at domain clondiag.com>
+Thomas Sicheritz-Ponten <thomas at domain cbs.dtu.dk>
+Frederic Sohm <fsms at domain users.sourceforge.net>
+Thomas Rosleff Soerensen <rosleff at domain mpiz-koeln.mpg.de>
+Johann Visagie <wjv at domain cityip.co.za>
+Dan Vogel <dmv at domain andrew.cmu.edu>
+David Weisman <david.weisman at domain acm.org>
+Bartek Wilczynski <bartek at domain rezolwenta.eu.org>
+Harry Zuzan <iliketobicycle at domain yahoo.ca>
--- /dev/null
+ Biopython License Agreement
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
--- /dev/null
+Metadata-Version: 1.0
+Name: biopython
+Version: 1.50
+Summary: Freely available tools for computational molecular biology.
+Home-page: http://www.biopython.org/
+Author: The Biopython Consortium
+Author-email: biopython@biopython.org
+License: UNKNOWN
+Download-URL: http://biopython.org/DIST/
+Description: UNKNOWN
+Platform: UNKNOWN
--- /dev/null
+#### THIS IS A REDUCED DESTRIBUTION OF BIOPYTHON ####
+
+**Biopython README file**
+
+ "The Biopython Project":http://www.biopython.org/ is an
+international association of developers of freely available Python
+tools for computational molecular biology.
+
+biopython.org provides an online resource for modules, scripts, and
+web links for developers of Python-based software for life science
+research. Thanks to bioperl, we can also provide web, FTP and CVS
+space for individuals and organizations wishing to distribute or
+otherwise make available standalone scripts & code.
+
+This Biopython package is made available under generous terms. Please
+see the LICENSE file for further details.
+
+
+**For the impatient**
+
+To build and install Biopython, download and unzip the source code,
+go to this directory at the command line, and type:
+
+python setup.py build
+python setup.py test
+python setup.py install
+
+**System Requirements**
+
+o "Python 2.3, 2.4, 2.5 or 2.6":http://www.python.org/
+ Note that Biopython 1.50 is expected to the our final release to support
+ Python 2.3. Given that Python 2.6 is still very new, it would be prudent
+ to opt for Python 2.5 or 2.4 at this time.
+
+o "NumPy":http://numpy.scipy.org/ (optional, but strongly recommended)
+ This package is only used in the computationally-oriented modules.
+ It is required for Bio.Cluster, Bio.PDB and a few other modules. If you
+ think you might need these modules, then please install NumPy first BEFORE
+ installing Biopython. The older Numeric library is no longer supported in
+ Biopython.
+
+o "ReportLab":http://www.reportlab.org/downloads.html (optional)
+ This package is only used in Bio.Graphics, so if you do not need this
+ functionality, you will not need to install this package. You can install
+ it later if needed.
+
+o "psycopg":http://initd.org/software/psycopg/ (optional) or
+ "pgdb":http://www.druid.net/pygresql/ (optional)
+ These packages are used by BioSQL to access a PostgreSQL database.
+
+o "MySQLdb":http://sourceforge.net/projects/mysql-python (optional)
+ This package is used by BioSQL or Bio.GFF to access a MySQL database.
+
+o "mxTextTools":http://www.egenix.com/files/python/mxTextTools.html (unlikely)
+ You probably won't need mxTextTools. This was used in some of Biopython's
+ older parsers, and Martel/Mindy, but these have all been deprecated now.
+
+In addition there are a number of useful third party tools you may wish to
+install such as standalone NCBI BLAST or ClustalW.
+
+
+**Installation**
+
+*** Make sure that Python is installed correctly ***
+
+Installation should be as simple as going to the biopython source code
+directory, and typing:
+
+ 'python setup.py build'
+ 'python setup.py test'
+ 'sudo python setup.py install'
+
+If you need to do additional configuration, e.g. changing the base
+directory, please type 'python setup.py', or see the documentation for
+Distutils.
+
+
+**Testing**
+
+Biopython includes a suite of regression tests to check if everything is
+running correctly. To do the tests, go to the biopython source code directory
+and type:
+
+ 'python setup.py test'
+
+Do not panic if you see messages warning of skipped tests:
+ test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
+
+This most likely means that a package is not installed. You can
+ignore this if it occurs in the tests for a module that you were not
+planning on using. If you did want to use that module, please install
+the required dependency and re-run the tests.
+
+
+**Bugs**
+
+While we try to ship a robust package, bugs inevitably pop up. If you
+are having problems that might be caused by a bug in Biopython, it is
+possible that it has already been identified. Search the
+"bug database":http://bugzilla.open-bio.org/ and mailing lists
+to see if it has already been reported (and hopefully fixed).
+
+If you suspect the problem lies within a parser, it is likely that the
+data format has changed and broken the parsing code. (The BLAST and
+GenBank formats seem to be particularly fragile.) Thus, the parsing
+code in Biopython is sometimes updated faster than we can build Biopython
+releases. You can get the most recent parser by pulling the relevant
+files (e.g. the ones in Bio.SeqIO or Bio.Blast) out of
+"anonymous cvs":http://cvs.biopython.org/ .
+However, be careful when doing this, because the code in CVS is not as
+well-tested as released code, and may contain new dependencies.
+
+Finally, you can send a bug report to the bug database or
+biopython@biopython.org. In the bug report, please let us know 1)
+which operating system and hardware you are using, 2) Python version,
+3) Biopython version (or CVS version/date), 4) traceback that occurs,
+5) offending code, and 6) data file that causes the problem.
+
+
+
+**Contributing, Bug Reports**
+
+Biopython is run by volunteers from all over the world, with many
+types of backgrounds. We are always looking for people interested in
+helping with code development, web-site management, documentation
+writing, technical administration, and whatever else comes up.
+
+If you wish to contribute, please visit the
+"web site":http://www.biopython.org
+and join our "mailing list":http://biopython.org/wiki/Mailing_lists
+
+
+
+**Distribution Structure**
+
+README -- This file.
+
+NEWS -- Release notes and news
+
+LICENSE -- What you can do with the code.
+
+CONTRIB -- An (incomplete) list of people who helped Biopython in
+ one way or another.
+
+DEPRECATED -- Contains information about modules in Biopython that are
+ removed or no longer recommended for use, and how to update
+ code that uses those modules.
+
+MANIFEST.in -- Tells distutils what files to distribute
+
+setup.py -- Installation file.
+
+Bio/ -- The main code base code.
+
+Martel/ -- Code for the Martel parsing system, once used in many
+ Biopython parsers but now deprecated.
+
+BioSQL/ -- Code for using Biopython with BioSQL databases.
+
+Doc/ -- Documentation.
+
+Scripts/ -- Miscellaneous, possibly useful, standalone scripts
+
+Tests/ -- Regression testing code
--- /dev/null
+> Foobar_dundeefriends_COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, 350-391, 429-485, 497-506, 539-547
+mtadgprellqlraavrhrpqdfvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghaledagqaeaaaaaytraHQLLPEEPYItaqllnwrrrlcdwraldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
+> Foobar_dundeefriends_REM465 355-368
+mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+> Foobar_dundeefriends_HOTLOOPS 190-204
+mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+
+> Foobar_COILS 32-40, 65-73, 85-133, 156-165, 200-256, 263-304, 342-398, 410-419, 452-460
+mgdttagemavqrglalhqqrhaeaavllqqASDAAPEHPgialwlhaledagqaeaaaaytraHQLLPEEPYitaqllnavaqGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
+> Foobar_REM465 1-11, 268-281
+MGDTTAGEMAVqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedasaaesvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+> Foobar_HOTLOOPS 100-118
+mgdttagemavqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedaSAAESVRPLAPTRVRSKGPlrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+
+> dundeefriends_COILS 33-40, 49-57, 82-90, 99-112, 132-141, 163-192, 215-224, 259-315, 322-363, 401-457, 469-478
+mtadgprellqlraavrhrpqdvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghALEDHQLLPEEPYItaqldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrresi
+> dundeefriends_REM465 327-340
+mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
+> dundeefriends_HOTLOOPS 162-176
+mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
+
--- /dev/null
+/********************************************************/
+/* ____ _ _____ __ __ ____ _ _ _____ */
+/* | _ \(_)___| ____| \/ | __ )| | / | |___ / */
+/* | | | | / __| _| | |\/| | _ \| | | | |_ \ */
+/* | |_| | \__ \ |___| | | | |_) | |___ | |_ ___) | */
+/* |____/|_|___/_____|_| |_|____/|_____| |_(_)____/ */
+/* DisEMBL is Copyright (C) 2003 */
+/* Lars Juhl Jensen & Rune Linding - EMBL */
+/* Licensed under GPL */
+/********************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/* Define size of the alphabet */
+#define na 21
+
+/* Define max number of neurons */
+#define mw 41
+#define mh 30
+
+#include "russel.h"
+#include "bfactor.h"
+#include "missing.h"
+
+float sigmoid[256] = {
+ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
+ 0.000000, 0.000000, 0.000000, 0.000000, 0.000001, 0.000001, 0.000001, 0.000001,
+ 0.000001, 0.000001, 0.000001, 0.000001, 0.000001, 0.000002, 0.000002, 0.000002,
+ 0.000002, 0.000003, 0.000003, 0.000003, 0.000004, 0.000004, 0.000005, 0.000005,
+ 0.000006, 0.000007, 0.000008, 0.000009, 0.000010, 0.000011, 0.000013, 0.000015,
+ 0.000017, 0.000019, 0.000021, 0.000024, 0.000028, 0.000031, 0.000035, 0.000040,
+ 0.000045, 0.000051, 0.000058, 0.000066, 0.000075, 0.000085, 0.000096, 0.000109,
+ 0.000123, 0.000140, 0.000158, 0.000180, 0.000203, 0.000231, 0.000261, 0.000296,
+ 0.000335, 0.000380, 0.000431, 0.000488, 0.000553, 0.000626, 0.000710, 0.000804,
+ 0.000911, 0.001032, 0.001170, 0.001325, 0.001501, 0.001701, 0.001927, 0.002183,
+ 0.002473, 0.002801, 0.003173, 0.003594, 0.004070, 0.004610, 0.005220, 0.005911,
+ 0.006693, 0.007577, 0.008577, 0.009708, 0.010987, 0.012432, 0.014064, 0.015906,
+ 0.017986, 0.020332, 0.022977, 0.025957, 0.029312, 0.033086, 0.037327, 0.042088,
+ 0.047426, 0.053403, 0.060087, 0.067547, 0.075858, 0.085099, 0.095349, 0.106691,
+ 0.119203, 0.132964, 0.148047, 0.164516, 0.182426, 0.201813, 0.222700, 0.245085,
+ 0.268941, 0.294215, 0.320821, 0.348645, 0.377541, 0.407333, 0.437823, 0.468791,
+ 0.500000, 0.531209, 0.562177, 0.592667, 0.622459, 0.651355, 0.679179, 0.705785,
+ 0.731059, 0.754915, 0.777300, 0.798187, 0.817574, 0.835484, 0.851953, 0.867036,
+ 0.880797, 0.893309, 0.904651, 0.914901, 0.924142, 0.932453, 0.939913, 0.946597,
+ 0.952574, 0.957912, 0.962673, 0.966914, 0.970688, 0.974043, 0.977023, 0.979668,
+ 0.982014, 0.984094, 0.985936, 0.987568, 0.989013, 0.990292, 0.991423, 0.992423,
+ 0.993307, 0.994089, 0.994780, 0.995390, 0.995930, 0.996406, 0.996827, 0.997199,
+ 0.997527, 0.997817, 0.998073, 0.998299, 0.998499, 0.998675, 0.998830, 0.998968,
+ 0.999089, 0.999196, 0.999290, 0.999374, 0.999447, 0.999512, 0.999569, 0.999620,
+ 0.999665, 0.999704, 0.999739, 0.999769, 0.999797, 0.999820, 0.999842, 0.999860,
+ 0.999877, 0.999891, 0.999904, 0.999915, 0.999925, 0.999934, 0.999942, 0.999949,
+ 0.999955, 0.999960, 0.999965, 0.999969, 0.999972, 0.999976, 0.999979, 0.999981,
+ 0.999983, 0.999985, 0.999987, 0.999989, 0.999990, 0.999991, 0.999992, 0.999993,
+ 0.999994, 0.999995, 0.999995, 0.999996, 0.999996, 0.999997, 0.999997, 0.999997,
+ 0.999998, 0.999998, 0.999998, 0.999998, 0.999999, 0.999999, 0.999999, 0.999999,
+ 0.999999, 0.999999, 0.999999, 0.999999, 0.999999, 1.000000, 1.000000, 1.000000,
+ 1.000000, 1.000000, 1.000000, 1.000000, 1.000000, 1.000000, 1.000000, 1.000000
+};
+
+
+
+
+/*
+ * Perform feed forward evaluation of a neural network on a sequence window.
+ */
+
+float feed_forward(int const *s, float const w[], int nw, int nh) {
+
+ float h[mh], o[2], x;
+ int i, j;
+
+ /* Shift input window to match network window size */
+ s += (mw-nw)/2;
+
+ /* Feed input values to hidden layer making use of sparse encoding */
+ for (i = 0; i < nh; ++i) {
+ x = w[(na*nw+1)*(i+1)-1];
+ for (j = 0; j < nw; ++j) {
+ x += w[(na*nw+1)*i+na*j+s[j]];
+ }
+ if (x <= -16) {
+ h[i] = 0;
+ } else if (x >= 16) {
+ h[i] = 1;
+ } else {
+ h[i] = sigmoid[(int)(8*x+128)];
+ }
+ }
+
+ /* Feed hidden layer values to output layer */
+ for (i = 0; i <= 1; ++i) {
+ x = w[(na*nw+1)*nh+(nh+1)*(i+1)-1];
+ for (j = 0; j < nh; ++j) {
+ x += w[(na*nw+1)*nh+(nh+1)*i+j]*h[j];
+ }
+ if (x <= -16) {
+ o[i] = 0;
+ } else if (x >= 16) {
+ o[i] = 1;
+ } else {
+ o[i] = sigmoid[(int)(8*x+128)];
+ }
+ }
+
+ /* Combine the scores from the two output neurons */
+ return((o[0]+1-o[1])/2);
+
+}
+
+
+
+
+/*
+ * Calculate and print scores for a sequence window.
+ */
+
+void predict(int const *s) {
+
+ float sm, sb, sr;
+
+ if (s[(mw-1)/2] == na-1) {
+ return;
+ }
+
+ sr = 0;
+ sr += feed_forward(s, r19_1, 19, 30);
+ sr += feed_forward(s, r19_2, 19, 30);
+ sr += feed_forward(s, r19_3, 19, 30);
+ sr += feed_forward(s, r19_4, 19, 30);
+ sr += feed_forward(s, r19_5, 19, 30);
+ sr /= 5;
+ sr = 0.07387214+0.8020778*sr;
+
+ sb = 0;
+ sb += feed_forward(s, b41_1, 41, 5);
+ sb += feed_forward(s, b41_2, 41, 5);
+ sb += feed_forward(s, b41_3, 41, 5);
+ sb += feed_forward(s, b41_4, 41, 5);
+ sb += feed_forward(s, b41_5, 41, 5);
+ sb /= 5;
+ sb = 0.08016882+0.6282424*sb;
+
+ sm = 0;
+ sm += feed_forward(s, m9_1, 9, 30);
+ sm += feed_forward(s, m9_2, 9, 30);
+ sm += feed_forward(s, m9_3, 9, 30);
+ sm += feed_forward(s, m9_4, 9, 30);
+ sm += feed_forward(s, m9_5, 9, 30);
+ sm += feed_forward(s, m21_1, 21, 30);
+ sm += feed_forward(s, m21_2, 21, 30);
+ sm += feed_forward(s, m21_3, 21, 30);
+ sm += feed_forward(s, m21_4, 21, 30);
+ sm += feed_forward(s, m21_5, 21, 30);
+ sm /= 10;
+
+ printf("%f\t%f\t%f\n", sr, sr*sb, sm);
+
+}
+
+int main(int ARGC, char *ARGV[]) {
+
+ char *alphabet = strdup("FIVWMLCHYAGNRTPDEQSK");
+
+ char *p;
+ int c, i, j, s[mw];
+
+ for (i = 0; i < mw; ++i) {
+ s[i] = na-1;
+ }
+
+ while (!feof(stdin)) {
+
+ c = fgetc(stdin);
+ p = strchr(alphabet, c);
+ if (p != NULL) {
+ for (i = 1; i < mw; ++i) {
+ s[mw-i] = s[mw-i-1];
+ }
+ s[0] = p-alphabet;
+ predict(s);
+ } else if ((char)c == '\n') {
+ for (i = 0; i < (mw-1)/2; i++) {
+ for (j = 1; j < mw; ++j) {
+ s[mw-j] = s[mw-j-1];
+ }
+ s[0] = na-1;
+ predict(s);
+ }
+ }
+
+ }
+
+ return(0);
+
+}
--- /dev/null
+float const m9_1[(na*9+1)*30+(30+1)*2] = {
+ -0.21418, -0.20201, 0.05376, 0.03406, 0.04926,
+ -0.00037, 0.07708, -0.08915, -0.21309, -0.23197,
+ -0.13159, 0.09620, -0.04455, -0.16529, 0.04997,
+ -0.01682, 0.10539, -0.18160, -0.17570, -0.04728,
+ 0.13071, -0.05832, 0.06565, -0.07643, -0.15145,
+ -0.17961, -0.01486, 0.08782, -0.07387, -0.25820,
+ 0.12729, -0.11325, -0.16613, -0.05051, 0.07967,
+ 0.01588, -0.14380, -0.19774, -0.06168, 0.07328,
+ 0.03866, 0.14042, 0.09744, 0.09189, -0.12094,
+ -0.04924, -0.13846, -0.01088, -0.09856, 0.04235,
+ 0.05199, -0.16803, -0.12083, 0.00589, -0.15699,
+ -0.18201, -0.08137, 0.17957, -0.20343, 0.16041,
+ 0.07707, -0.18664, -0.10641, 0.09412, -0.08846,
+ -0.21243, 0.02265, -0.07853, -0.22191, 0.00626,
+ 0.10344, -0.18445, -0.28258, 0.11100, -0.01220,
+ 0.04906, 0.13041, 0.07099, -0.07352, -0.06076,
+ 0.16519, -0.14975, -0.24272, -0.06301, -0.01819,
+ -0.05721, -0.15903, -0.20573, 0.09397, -0.35378,
+ -0.21107, 0.17154, 0.05831, -0.26282, -0.23669,
+ 0.08765, 0.02555, 0.07552, 0.10493, -0.12563,
+ -0.01379, 0.11708, -0.02902, -0.07874, 0.10000,
+ -0.18518, 0.14986, 0.03823, 0.04263, -0.13064,
+ -0.38500, 0.01024, 0.16321, 0.03016, -0.17490,
+ -0.16460, -0.24521, -0.20196, -0.19762, -0.14934,
+ 0.09622, -0.19144, 0.10816, 0.05794, 0.01409,
+ 0.19796, -0.19354, 0.10151, -0.24439, -0.22607,
+ 0.10579, 0.05202, -0.19865, 0.07279, -0.20769,
+ -0.28501, -0.17248, -0.12752, 0.09705, 0.07721,
+ -0.15780, 0.13088, -0.03223, -0.02846, 0.05655,
+ -0.02243, -0.11474, -0.24133, -0.10300, -0.13722,
+ -0.13117, 0.00459, -0.00943, -0.00072, 0.10046,
+ -0.21117, -0.06756, -0.26482, -0.12936, 0.06681,
+ -0.04136, -0.07981, -0.20880, 0.22096, 0.13552,
+ 0.04555, -0.13814, -0.12721, -0.07494, -0.16510,
+ 0.08805, -0.20086, -0.05855, -0.07702, 0.04755,
+ 0.05945, 0.04925, -0.27607, -0.24938, -0.06274,
+ -0.29828, -0.03914, -0.16437, -0.12147, -0.11222,
+ -0.28668, 0.04654, 0.11448, 0.26429, -0.91718,
+ -0.20790, 0.01418, -0.15750, -0.15146, -0.17974,
+ 0.11118, -0.13361, 0.06443, 0.04366, -0.20717,
+ -0.13382, -0.09952, -0.21420, -0.14534, 0.07033,
+ 0.05249, 0.04438, -0.12207, -0.15042, -0.17814,
+ 0.20284, -0.19046, -0.13475, 0.04797, 0.06155,
+ 0.04581, -0.17437, -0.10893, 0.11825, -0.13528,
+ 0.03866, 0.03279, 0.06037, -0.18997, -0.12208,
+ 0.03586, 0.00796, 0.01092, -0.08870, -0.09358,
+ 0.00766, 0.09292, -0.14912, 0.05572, -0.11971,
+ -0.18084, 0.08727, 0.03747, 0.06564, 0.07344,
+ -0.14830, -0.20625, -0.21734, 0.08951, 0.05952,
+ -0.10898, -0.13783, 0.05878, -0.01100, 0.09719,
+ -0.12701, 0.02335, 0.08107, -0.18007, 0.10287,
+ 0.00437, -0.15302, -0.11284, -0.23607, -0.16067,
+ -0.06380, 0.03125, -0.04880, -0.14999, -0.15055,
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+ -0.37699, 0.14074, 0.21310, -0.24086, 0.32465,
+ 0.94338, -0.20359, 0.14895, -0.69101, -0.31104,
+ -0.46812, 0.41142, 0.37758, 0.47163, 0.04299,
+ -0.68091, 0.46915, -0.62640, -0.44085, -0.13625,
+ 0.10252, -0.47667, -0.58135, 0.57862, 0.34699,
+ 0.14150, -0.03660, -0.28482, 0.18328, -0.03485,
+ -0.37111, -0.39748, -0.22795, 0.04830, 0.35482,
+ 0.17904, -0.16353, -0.00796, -0.40013, 0.04400,
+ -0.00331, -0.08390, -0.23408, -0.30109, 0.63808,
+ 0.16843, -0.23175, -0.03541, 0.01955, -0.00989,
+ 0.72414, -0.15830, 0.06150, -0.32733, -0.18406,
+ 0.29802, -0.04044, -0.96513, 0.19447, 0.13861,
+ -0.07212, -0.26875, -0.52711, 0.37108, -0.48481,
+ -0.54811, 0.35360, 0.18490, 0.07876, -0.32561,
+ -0.59271, 0.26276, -0.35161, 0.30048, -0.87071,
+ -0.59032, 0.44131, -0.41972, -0.09054, 0.06955,
+ -0.17841, 0.16894, -0.20526, -0.68389, 0.72861,
+ 0.38571, 0.29360, 0.15380, -0.15740, 0.10000,
+ -0.02424, 0.28985, 0.39617, -0.62032, 0.04991,
+ 0.31555, -0.72342, 0.38078, -0.31483, -0.05883,
+ -0.88399, -0.43016, 0.58377, 0.09669, -0.30521,
+ 0.10514, -0.12352, -0.04909, 0.01416, -0.35617,
+ 0.49630, -0.48378, -0.53258, -0.65564, -0.69949,
+ 0.02490, -0.28422, -0.41819, 0.23795, -0.15333,
+ -0.29790, 0.64139, -0.55015, -0.41216, 0.03186,
+ 0.26854, 0.23136, 0.65578, 0.50001, -0.14411,
+ 0.06268, 0.21567, -0.32027, 0.13996, -0.48033,
+ -0.15283, -0.01604, -0.49481, -0.14776, 0.61544,
+ -0.58246, -1.01118, 0.00220, -0.65053, 0.07753,
+ 0.87804, -0.03101, -0.55203, 0.18904, -0.26171,
+ 0.12259, 0.73892, -0.02420, -0.15628, 0.02631,
+ 0.40800, 0.22668, -0.33960, -0.94898, -0.53459,
+ 0.00415, 0.19055, -0.20410, -0.10858, -0.55965,
+ 0.01521, 0.24312, 0.18959, -0.64922, -0.11757,
+ -0.49159, -0.10335, 0.29353, 0.85492, -1.36143,
+ 0.35021, 0.13881, 0.38089, -0.03402, 2.31461,
+ 0.23860, 0.51526, -2.01425, -0.28382, -0.09668,
+ -0.83361, -2.25507, -1.02714, -0.91478, -0.31856,
+ 0.20533, 0.15766, -0.18898, 0.20941, -0.36035,
+ -0.15821, 0.37470, -0.02832, -0.66132, 0.38029,
+ 2.19014, -1.05102, 0.02196, -1.28203, 1.73948,
+ 0.16866, -0.35460, -0.14326, -0.37944, 0.03473,
+ -2.31401, -0.24075, -0.51171, 2.01280, 0.28268,
+ 0.10182, 0.83324, 2.25482, 1.02375, 0.91585,
+ 0.31926, -0.20752, -0.15383, 0.19537, -0.21079,
+ 0.35929, 0.16309, -0.36759, 0.02984, 0.66231,
+ -0.38061, -2.19069, 1.05078, -0.01769, 1.28248,
+ -1.73854, -0.17271
+};
+
+float const m9_2[(na*9+1)*30+(30+1)*2] = {
+ -0.14555, -0.49540, 0.35208, 0.10617, 0.02545,
+ -0.32616, 0.07916, -0.15048, -0.39315, -0.21769,
+ -0.03519, 0.13267, 0.04831, -0.13893, 0.03082,
+ 0.15822, 0.17413, -0.21655, -0.40266, -0.00613,
+ 0.18444, -0.09910, -0.05778, -0.30027, -0.05099,
+ -0.17173, -0.00323, 0.02322, -0.19732, -0.46162,
+ 0.06402, -0.19283, -0.07371, 0.19217, 0.13069,
+ 0.06656, 0.01450, -0.02034, -0.16351, -0.00862,
+ 0.25314, 0.01996, 0.28373, 0.22210, -0.26757,
+ -0.21997, -0.05906, 0.20833, -0.08656, 0.04395,
+ 0.00755, -0.33460, -0.09115, -0.10662, 0.11294,
+ -0.09075, -0.15760, 0.27203, -0.24942, 0.12364,
+ -0.00274, -0.39172, -0.25000, 0.04580, -0.11336,
+ -0.44158, -0.02151, 0.04779, -0.39929, 0.03841,
+ 0.07306, 0.14755, -0.28579, 0.46750, -0.09063,
+ 0.01268, 0.18309, 0.11848, -0.34774, 0.01538,
+ 0.22395, -0.08726, -0.51254, -0.10334, -0.23421,
+ -0.05175, -0.20099, -0.14142, 0.20267, -0.75424,
+ -0.16257, 0.34992, 0.04704, -0.21061, 0.04246,
+ 0.10528, 0.09750, 0.02854, 0.08027, -0.18377,
+ -0.10894, 0.14850, 0.14228, -0.32171, 0.10000,
+ -0.14788, 0.38078, 0.40861, 0.06107, -0.02011,
+ -0.81887, 0.01522, 0.21453, 0.06827, -0.42783,
+ -0.22310, -0.22061, -0.01645, -0.45368, -0.47203,
+ 0.35016, -0.12778, 0.06253, 0.11504, -0.18301,
+ 0.20938, -0.24359, 0.11961, -0.27092, -0.26557,
+ 0.00933, 0.02336, -0.20384, 0.10244, -0.06362,
+ -0.19828, -0.19619, 0.10908, -0.07794, -0.15034,
+ -0.51391, 0.41647, 0.13745, 0.12490, 0.19171,
+ -0.32930, -0.14660, -0.55642, -0.16383, -0.41520,
+ -0.19018, 0.07169, 0.34013, -0.00835, 0.18987,
+ -0.07643, 0.04837, -0.17857, -0.13678, -0.41554,
+ -0.05782, 0.00499, -0.02245, 0.32448, 0.15979,
+ 0.11860, -0.24187, -0.22101, -0.10890, -0.46436,
+ 0.21756, -0.21039, 0.12446, -0.28111, 0.08159,
+ 0.11976, -0.04027, -0.15388, -0.04728, -0.16144,
+ -0.42620, -0.16754, -0.03391, -0.28643, -0.18752,
+ -0.36682, 0.26203, 0.24480, 0.25799, -1.07673,
+ -0.15444, 0.01620, -0.18382, -0.13235, -0.12448,
+ -0.01408, -0.11122, 0.08993, 0.05027, -0.16053,
+ -0.16014, -0.14820, -0.14961, -0.14536, 0.05329,
+ 0.03686, 0.03707, -0.11410, -0.15298, -0.14688,
+ 0.14032, -0.15462, -0.17296, 0.00786, 0.06704,
+ 0.06036, -0.18126, -0.11226, 0.10047, -0.13856,
+ 0.01585, 0.03909, 0.05642, -0.14591, -0.14401,
+ 0.04782, 0.06754, 0.05027, -0.14025, -0.13142,
+ 0.04198, 0.09223, -0.16237, 0.02227, -0.18718,
+ -0.12582, 0.06098, -0.01417, 0.07788, 0.09354,
+ -0.14570, -0.16215, -0.15546, 0.04445, 0.04192,
+ -0.14548, -0.13618, 0.04682, 0.06690, 0.08399,
+ -0.13407, 0.07164, 0.08333, -0.15694, 0.01447,
+ 0.00894, -0.12761, -0.13666, -0.18161, -0.11911,
+ -0.10566, 0.02862, 0.04187, -0.15829, -0.13115,
+ 0.05081, 0.02533, 0.05934, -0.12012, 0.04153,
+ 0.07561, 0.06050, -0.14644, -0.09839, 0.04542,
+ 0.04366, 0.01788, 0.06461, -0.13192, -0.17005,
+ 0.07586, 0.09398, 0.03438, 0.02223, -0.16955,
+ -0.14342, 0.05151, 0.05425, 0.04661, -0.14397,
+ -0.14985, 0.08221, -0.16152, -0.13726, -0.10000,
+ -0.15336, 0.02349, -0.18510, -0.14839, -0.13666,
+ 0.02320, -0.12956, -0.08282, 0.03473, -0.16889,
+ 0.02999, 0.06375, 0.05580, 0.05912, 0.04763,
+ -0.13779, -0.15796, 0.06684, -0.16245, 0.04950,
+ -0.06600, 0.02948, 0.02113, -0.17308, -0.13483,
+ -0.12549, -0.17617, 0.06981, -0.09653, 0.04510,
+ 0.02546, 0.02970, -0.12794, -0.14021, 0.04080,
+ -0.12733, 0.04760, 0.06216, 0.06023, -0.14581,
+ 0.05429, -0.11331, -0.14326, -0.17102, 0.01685,
+ 0.06125, 0.07530, 0.00528, 0.08244, 0.09747,
+ -0.15163, 0.01385, -0.16443, -0.12388, -0.14068,
+ 0.05198, 0.05656, 0.05977, -0.14306, -0.13893,
+ 0.04583, 0.04216, -0.10692, 0.03373, -0.15691,
+ 0.02065, 0.06484, -0.13553, -0.20162, 0.07999,
+ 0.09385, 0.04373, -0.17366, -0.16947, -0.14419,
+ 0.05020, 0.05815, 0.02942, -0.14132, -0.13044,
+ 0.06861, 0.04979, 0.03934, 0.14546, -0.87779,
+ -0.10962, -0.05312, -0.26638, 0.02498, -0.17766,
+ -0.03492, -0.10693, -0.08257, -0.05811, -0.17917,
+ 0.17686, -0.19183, 0.01530, -0.18102, 0.06739,
+ 0.02463, 0.09814, -0.03662, 0.10045, -0.02181,
+ 0.25366, -0.22756, -0.10457, -0.02816, -0.16626,
+ -0.18951, -0.12019, 0.01963, 0.17246, -0.02999,
+ -0.23043, -0.03293, -0.08898, 0.08795, -0.05666,
+ 0.02878, 0.05279, -0.03158, 0.08766, -0.09396,
+ 0.03491, -0.02213, -0.27608, -0.01467, 0.04449,
+ -0.22418, 0.05508, -0.29716, -0.15217, -0.03150,
+ -0.21059, -0.25251, 0.06741, -0.13406, -0.07089,
+ -0.08063, -0.10226, -0.05907, 0.08326, 0.11286,
+ 0.05484, 0.04717, -0.09814, -0.12812, -0.23755,
+ 0.05227, -0.03717, 0.03594, -0.09067, 0.03239,
+ 0.19545, -0.01474, -0.04411, 0.16455, 0.00393,
+ -0.15145, -0.08727, 0.12280, 0.10704, 0.02594,
+ 0.13103, 0.23921, -0.02944, -0.02721, -0.31472,
+ -0.02711, -0.00273, -0.18807, -0.14491, -0.14176,
+ 0.01311, 0.01104, -0.19707, -0.14553, -0.15573,
+ -0.14074, 0.08579, 0.07649, -0.17553, -0.08485,
+ -0.07845, 0.14031, 0.17910, -0.14386, 0.10000,
+ -0.26817, -0.36487, 0.06548, -0.07809, 0.04699,
+ -0.34044, 0.00285, -0.00201, -0.25319, -0.00263,
+ -0.08681, -0.12777, -0.11281, 0.02158, 0.06397,
+ 0.12425, 0.09783, 0.11186, 0.19392, 0.06872,
+ 0.30415, -0.23329, -0.06169, 0.05090, 0.01573,
+ -0.19495, -0.33409, -0.19088, 0.11980, 0.03647,
+ -0.11154, -0.16678, -0.15282, 0.05913, -0.05144,
+ -0.14021, 0.00028, -0.06063, 0.13205, -0.01253,
+ 0.02657, 0.13473, -0.03434, -0.28409, -0.15262,
+ -0.17858, -0.17103, -0.08597, 0.05422, 0.09827,
+ -0.04743, -0.01746, -0.22920, 0.08876, -0.00991,
+ 0.05634, -0.11450, -0.06899, -0.02841, -0.07066,
+ 0.15135, 0.14763, 0.16051, 0.02274, -0.32150,
+ -0.02923, -0.02297, -0.11655, -0.19393, 0.04079,
+ -0.10286, 0.00012, 0.13861, 0.02513, 0.01002,
+ -0.17980, 0.01810, 0.06559, -0.23292, 0.12862,
+ 0.06109, -0.08257, -0.19409, 0.22855, -0.96396,
+ 0.05050, 0.03605, 0.03365, 0.08133, -0.11812,
+ -0.17258, 0.09539, 0.08765, -0.13676, 0.04221,
+ 0.04788, 0.06149, -0.13008, -0.13892, -0.14729,
+ -0.14515, 0.03660, 0.07241, 0.03424, -0.15544,
+ 0.13766, 0.05148, -0.15183, -0.13419, 0.08457,
+ 0.07325, 0.02862, -0.11327, 0.09085, -0.13350,
+ -0.15871, 0.03640, 0.06960, 0.05313, 0.06493,
+ 0.06021, 0.03777, 0.04065, 0.07460, 0.03839,
+ -0.14684, -0.09344, 0.04897, 0.04428, -0.14317,
+ -0.12257, -0.11792, -0.00052, -0.11430, -0.10153,
+ 0.06143, 0.02668, 0.03440, -0.12196, 0.07511,
+ 0.07103, 0.07237, -0.13336, -0.16002, 0.07600,
+ 0.03060, 0.04545, 0.10190, -0.14644, 0.05317,
+ 0.04346, 0.07346, 0.07858, -0.16394, 0.08273,
+ -0.10956, -0.13048, 0.01616, -0.14580, 0.05942,
+ -0.13810, -0.13649, 0.05677, 0.04994, -0.15251,
+ 0.07047, 0.05295, -0.14955, -0.09098, 0.05231,
+ 0.04931, 0.03252, 0.07838, -0.11785, -0.17845,
+ -0.12090, -0.10490, 0.05542, -0.16832, -0.13699,
+ -0.13747, -0.13164, -0.14968, -0.13731, -0.14060,
+ -0.15008, 0.06809, -0.14386, 0.05550, -0.10000,
+ 0.04365, 0.04161, -0.14509, -0.13052, 0.07046,
+ 0.00110, -0.12159, -0.10499, -0.13215, -0.16292,
+ 0.04029, 0.06371, 0.05981, 0.05058, -0.13147,
+ 0.05139, -0.14032, -0.12314, 0.06399, -0.13892,
+ -0.08200, 0.05288, 0.03682, -0.16199, -0.12477,
+ 0.07682, -0.18216, 0.07999, -0.10989, -0.12805,
+ -0.15186, 0.03960, 0.06638, 0.04663, -0.13408,
+ -0.12936, -0.14467, -0.15205, -0.11851, -0.12673,
+ -0.15258, 0.09102, 0.05140, 0.03660, -0.16075,
+ -0.12041, -0.12643, 0.03054, -0.11299, 0.07477,
+ -0.13777, -0.16637, -0.15190, -0.12668, 0.04095,
+ -0.13841, -0.13500, -0.13722, -0.13068, -0.13105,
+ -0.13448, -0.13815, -0.11265, -0.13676, -0.14703,
+ 0.03318, 0.07630, -0.10573, -0.17331, -0.11549,
+ -0.11659, -0.14075, 0.03734, -0.15323, -0.13501,
+ 0.05219, -0.13718, -0.13015, -0.14043, 0.03714,
+ -0.12957, 0.05368, 0.03863, 0.10606, -0.93016,
+ -0.90088, 0.78861, -1.17675, 0.15134, 0.34789,
+ -0.95572, -0.32385, 0.57019, -0.59101, 0.78534,
+ -0.11482, -0.34846, 0.36621, -0.41256, -0.11284,
+ -0.70448, -0.33039, 0.03184, -0.03590, 0.40469,
+ 0.26110, -0.58298, 0.88206, -0.81162, 0.39521,
+ 0.29766, -0.74712, -0.04326, 0.73242, -0.41619,
+ 0.17202, -0.64227, -0.14138, 0.47369, 0.29787,
+ 0.02292, -0.55201, -0.66188, 0.06142, -0.46856,
+ 0.39740, -0.36625, -0.79993, 0.53238, -0.36004,
+ 0.56412, 0.21403, -0.60168, -0.31090, 0.52622,
+ -0.89115, -0.02154, 0.11444, -0.31760, 0.73070,
+ -0.40024, 0.06902, -0.26779, -0.69560, 0.20078,
+ 0.11434, 0.49865, 0.00526, -0.55084, -0.30110,
+ -0.41042, -0.08765, -0.10626, 0.06707, -0.23034,
+ 0.91926, -0.21446, 0.01226, -0.12033, -0.20287,
+ 0.47254, -0.08702, 0.00325, -0.47258, -1.08643,
+ 0.45510, 0.66520, -0.09850, 0.08519, -0.32591,
+ -0.69987, 0.23768, 0.06512, 0.36398, -0.48653,
+ -0.90481, 0.61437, -0.25619, 0.53393, -0.15537,
+ 0.09417, 0.15002, -0.28753, -0.47492, -0.61721,
+ -0.60358, 0.67294, 0.16544, 0.13583, 0.10000,
+ 0.26795, -0.62466, 0.03843, -0.35730, 0.43176,
+ -0.33980, -0.82734, 0.32782, -0.87066, 0.48329,
+ 0.84210, 0.24971, 0.22878, -0.19852, -0.30999,
+ -0.61638, -0.70755, 0.46067, -0.47470, 0.46966,
+ 0.24828, -0.54467, 0.80959, 0.05277, -0.20809,
+ 0.17010, -0.61661, -0.40277, 0.79659, -0.63066,
+ 0.60592, 0.21130, -0.70228, -0.03367, -0.35806,
+ -0.34663, -0.53780, -0.78183, 0.49130, -0.65212,
+ 0.65868, -0.25951, -0.31696, -0.31573, -0.35694,
+ -0.37157, 0.12474, 0.11405, -0.35541, 0.46316,
+ 0.18935, 0.14618, 0.52451, -0.47763, -0.21287,
+ 0.34326, -0.47484, -0.21331, -0.72074, 0.74418,
+ -0.25238, 0.38594, -0.24715, -0.77581, 0.08354,
+ -0.93746, -0.08534, 0.13795, -0.70638, -0.36740,
+ 0.17334, 0.32362, 0.35403, 0.60414, 0.32181,
+ -0.36595, 0.18352, -0.14420, -1.11348, -0.43058,
+ 1.01655, -0.06556, 0.29737, 0.41316, -1.78553,
+ -0.05594, -0.26080, -0.04569, 0.02825, -0.17620,
+ -0.25360, -0.11943, 0.12961, -0.23795, 0.05623,
+ 0.06433, -0.15747, -0.10241, -0.16364, 0.08332,
+ 0.03367, -0.14835, -0.07617, -0.12116, 0.05601,
+ 0.23707, -0.03362, -0.06759, -0.02989, 0.03484,
+ -0.17780, -0.07290, 0.06195, 0.18314, -0.18971,
+ 0.02691, 0.08711, -0.13492, 0.08988, -0.16134,
+ -0.14454, -0.10886, -0.08605, 0.07949, -0.05945,
+ 0.06339, 0.00937, -0.05473, -0.25434, -0.20765,
+ 0.01814, 0.04207, -0.10319, 0.06571, -0.02776,
+ -0.01329, 0.02117, -0.12009, -0.15274, 0.12359,
+ -0.15342, -0.12061, 0.11721, -0.10214, -0.07036,
+ 0.10899, -0.08523, -0.06283, -0.26067, -0.08292,
+ -0.03251, -0.18928, -0.16744, -0.08474, -0.17503,
+ 0.18892, -0.22205, -0.10554, -0.11163, 0.07820,
+ 0.10293, -0.13530, 0.05607, 0.06534, -0.11317,
+ 0.16206, 0.15469, -0.12824, -0.03057, -0.04820,
+ -0.23841, -0.01572, 0.02009, -0.12997, -0.06756,
+ 0.01447, -0.01320, -0.23277, -0.15131, -0.09169,
+ -0.11621, 0.07831, 0.07942, 0.04348, -0.12957,
+ 0.09650, -0.06672, 0.11969, 0.11920, -0.10000,
+ -0.05936, -0.24655, -0.20549, -0.24104, 0.02313,
+ -0.29886, 0.02552, 0.00054, -0.24991, -0.17583,
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+ -0.72775, 0.16465, -0.58383, -0.19959, -0.07207,
+ 0.27284, 0.45211, 0.37186, 0.11655, -0.12834,
+ 0.30355, 0.02207, 0.13791, 0.09007, -0.26309,
+ 0.02464, -0.10683, -0.93163, -0.20165, 0.27959,
+ -0.15537, -0.15507, -1.01467, 0.08943, 0.10000,
+ 0.09711, 0.50054, -0.07392, 0.24716, 0.50854,
+ -0.10063, -0.17276, -0.30287, -0.27006, -0.88000,
+ -0.18943, -0.00984, -0.22287, -0.18461, 0.27805,
+ -0.01126, -0.10629, -0.26884, 0.07390, -0.35278,
+ -0.32723, 0.40586, -0.05258, 0.53130, 0.31409,
+ 0.30153, 0.11565, -0.27442, -0.31843, 0.42371,
+ -0.26722, 0.33460, -0.22808, -0.23213, -0.45045,
+ -0.77855, -0.27004, 0.04258, -0.10731, -0.47633,
+ 0.11822, -0.10010, 0.05878, 0.62269, -0.36764,
+ 0.25321, 0.13606, -0.55353, -0.21237, 0.17618,
+ -0.16394, -0.38366, 0.16039, -0.09375, -0.02861,
+ -0.00824, 0.08974, 0.02922, -1.00212, -0.18758,
+ -0.28073, -0.06471, -0.14574, -0.29898, 0.28391,
+ -0.13617, -0.19722, -0.60626, -0.21081, 0.37298,
+ -0.38609, -0.19825, 0.45596, -0.07035, 0.37415,
+ 0.10068, 0.20469, -0.07917, -0.30379, -0.41013,
+ 0.53403, -0.63776, 0.10276, -0.65771, -1.28315,
+ -0.17270, -0.19115, 0.06505, 0.06925, 0.06785,
+ 0.00561, 0.07962, -0.12913, -0.13385, 0.02614,
+ 0.08020, -0.13285, 0.06725, -0.12265, 0.06895,
+ 0.04371, -0.19874, 0.08926, 0.05059, 0.01811,
+ 0.18522, -0.17616, -0.17134, -0.14272, 0.08125,
+ 0.04508, 0.01745, 0.08019, -0.08442, -0.14988,
+ 0.06270, -0.11594, -0.14039, 0.07227, 0.05847,
+ 0.05308, -0.18540, -0.14901, -0.10554, 0.04603,
+ -0.14935, -0.11080, 0.05444, -0.13952, -0.11400,
+ 0.05595, 0.07121, -0.18951, 0.07807, -0.09778,
+ 0.03231, 0.03096, -0.14504, 0.05635, -0.08744,
+ -0.13629, -0.13101, -0.13953, 0.00287, 0.08038,
+ 0.04928, 0.02898, -0.12501, -0.18788, -0.17682,
+ 0.07246, 0.05738, 0.05577, -0.25178, -0.13968,
+ -0.10199, -0.15613, 0.00494, 0.08496, 0.04396,
+ -0.10127, 0.08496, -0.11253, 0.05296, 0.03276,
+ -0.08679, 0.08885, -0.14013, 0.11218, -0.17181,
+ -0.14434, 0.02162, 0.06492, -0.13638, -0.20050,
+ 0.05863, -0.08461, -0.13229, 0.03026, -0.12739,
+ 0.04637, 0.08458, 0.03592, -0.14217, -0.13074,
+ -0.17365, -0.10904, -0.12813, -0.12407, -0.10000,
+ 0.03598, -0.17732, 0.03361, -0.16723, 0.06473,
+ -0.17448, -0.11722, 0.08881, 0.03293, -0.15188,
+ -0.12057, 0.06818, -0.14129, 0.03754, -0.12440,
+ -0.12307, -0.18267, 0.08799, -0.12835, 0.05765,
+ -0.06176, 0.04822, 0.01524, -0.20290, -0.13902,
+ -0.12294, -0.00379, -0.12870, 0.06157, -0.14435,
+ 0.09101, -0.10152, -0.10840, 0.05918, 0.04697,
+ 0.05090, -0.17969, 0.06802, 0.12374, 0.10751,
+ 0.03010, -0.13399, -0.16664, -0.17336, 0.02565,
+ -0.12389, -0.13611, -0.17275, 0.07292, -0.13693,
+ 0.03366, 0.00445, -0.14733, -0.12498, 0.04600,
+ -0.12817, -0.08667, -0.15515, -0.11938, 0.05842,
+ 0.08983, -0.08553, 0.06290, -0.11197, -0.00898,
+ 0.02816, 0.06440, -0.12007, -0.18966, -0.11759,
+ -0.14384, -0.11930, -0.10868, 0.07045, -0.11915,
+ 0.06164, 0.03087, 0.06832, -0.16203, -0.16492,
+ -0.15042, -0.12998, 0.01490, -0.05563, -0.97405,
+ 0.47013, 0.20199, -0.40231, -0.04020, 0.20269,
+ -0.29521, 0.07524, -0.20820, 0.21588, 0.22260,
+ -0.64417, -0.38383, 0.16001, 0.23764, -0.08184,
+ 0.21221, -0.14068, -0.35421, 0.24496, 0.19286,
+ -0.82795, -0.08985, 0.44459, 0.02048, -0.00671,
+ -0.11053, -0.15943, 0.24544, 0.32999, 0.03526,
+ -0.30207, -0.24853, -0.38288, 0.04223, -0.32660,
+ 0.15012, -0.04330, 0.08163, -0.45550, 0.11330,
+ -0.19230, -0.28696, -0.23258, 0.04173, -0.05917,
+ 0.17457, -0.04785, -0.13783, 0.07799, -0.19655,
+ 0.21099, 0.21702, 0.22063, 0.02342, -0.02465,
+ -0.13998, -0.07515, -0.48026, 0.16989, -0.12689,
+ -0.39953, 0.01942, 0.02203, 0.12177, 0.11698,
+ -0.29538, 0.31319, 0.12705, 0.29082, -0.19743,
+ -0.24794, 0.30506, -0.49127, 0.26765, 0.00935,
+ -0.15382, -0.07186, -0.27033, -0.35934, 0.06821,
+ -0.31728, -0.33447, -0.17853, -0.04820, -0.07426,
+ 0.12549, -0.07280, 0.39605, -0.34653, 0.43219,
+ 0.15404, -0.34741, 0.19266, 0.09891, -0.51637,
+ 0.14175, -0.36330, -0.30251, -0.04158, 0.01235,
+ 0.15218, -0.49341, -0.05233, -0.34354, -0.10000,
+ 0.11681, -0.11339, -0.14950, 0.10276, -0.17090,
+ -0.06320, -0.04046, -0.10642, -0.01096, 0.08065,
+ -0.07334, 0.03444, 0.08838, -0.28747, 0.25231,
+ -0.11061, -0.54274, 0.06079, -0.41184, -0.18190,
+ -0.42182, 0.18711, 0.49939, -0.42604, -0.06954,
+ 0.11496, 0.14044, 0.18008, 0.26480, 0.16272,
+ -0.58459, -0.10386, 0.06973, -0.08861, -0.29971,
+ 0.20304, -0.14766, -0.47480, -0.38123, -0.09893,
+ -0.09317, -0.00255, -0.04576, 0.10201, -0.36229,
+ 0.06874, 0.44147, 0.13990, -0.10835, -0.16812,
+ 0.23513, 0.01828, -0.13111, 0.09731, -0.22010,
+ -0.33957, -0.34943, -0.23183, -0.19988, 0.11467,
+ -0.11730, 0.23922, -0.13003, 0.05008, 0.12166,
+ -0.05750, 0.33932, 0.12721, -0.33582, 0.01867,
+ -0.10586, -0.21624, -0.05972, -0.31722, -0.20675,
+ -0.25764, 0.17125, 0.29557, 0.29956, -0.47486,
+ 0.09690, -0.19008, 0.12911, -0.57270, -1.08524,
+ 0.32601, 0.61139, -0.71128, -0.27636, -0.20469,
+ -0.00820, 0.19238, -0.30811, -0.35266, -0.42203,
+ -0.50321, -0.05483, -0.23524, 0.02679, -0.04051,
+ 0.40282, 0.20518, 0.05507, -0.15215, 0.19878,
+ 0.78131, 0.09340, -0.23034, -1.01347, -0.13472,
+ -0.10877, 0.27904, 0.08800, 0.13286, 0.27005,
+ -1.08120, 0.83629, -0.47231, -0.18619, -0.11681,
+ 0.36840, -0.15437, -0.32294, 0.52499, 0.27328,
+ -0.27444, -0.24102, -0.17698, -0.02480, -0.18505,
+ -0.32457, -0.23613, -0.34221, 0.11499, 0.33955,
+ 0.41785, -0.63604, 0.19166, -0.07917, 0.25924,
+ 0.12733, 0.14371, -0.24230, 0.05401, 0.22411,
+ 0.10844, -0.55114, -0.24657, 0.27400, -0.20464,
+ 0.48963, -0.04812, 0.22345, -0.90509, 0.01047,
+ 0.17891, -0.08868, -0.70545, 0.02427, 0.11652,
+ 0.20746, -0.63740, -0.37134, 0.49221, -0.12372,
+ 0.04306, 0.21928, -0.19857, -0.05162, -0.49179,
+ -0.02288, 0.16654, -0.35412, 0.16287, -0.48629,
+ -0.27085, 0.11031, -0.17846, -0.81459, 0.09099,
+ -0.18879, 0.38436, -0.30632, -0.98437, 1.29602,
+ 0.69794, 0.36965, -0.03593, -0.69042, 0.10000,
+ -0.10933, 0.36102, -0.15724, -0.35298, 0.30590,
+ 0.16818, -0.50499, 0.57962, 0.11954, -0.03637,
+ -0.70804, -0.48325, -0.47302, 0.16792, -0.61385,
+ 0.84764, -0.10860, -0.00603, 0.06045, -0.35016,
+ 0.24744, -0.20041, -0.82873, -0.56475, -0.36393,
+ -0.02933, -0.26176, -0.17802, 0.51237, 0.15424,
+ -0.52088, 0.59652, -0.47983, -1.00346, 0.38831,
+ 0.17728, -0.15975, 0.48664, 0.31181, 0.41242,
+ -0.19888, 0.10401, -0.68683, 0.03418, -0.09246,
+ 0.00044, 0.01980, -0.83598, 0.10027, 0.45888,
+ -0.62315, -0.50510, -0.52588, -0.57140, -0.36912,
+ 0.78200, 0.02980, -0.37722, 0.67269, -0.05731,
+ 0.76232, 0.13014, -0.19386, -0.27002, 0.00041,
+ 0.54037, 0.30467, -0.15448, -0.71707, -0.55151,
+ -0.18076, -0.01111, -0.49202, -0.33951, -0.14309,
+ -0.12104, -0.04910, 0.25213, -0.60087, 0.57440,
+ -0.09961, -0.00306, -0.08282, 0.49368, -1.34876,
+ 0.97697, -0.11959, 0.01335, 0.03874, 2.34524,
+ -0.18834, 0.80267, -2.61097, -0.07570, -0.22443,
+ -0.59297, -2.15776, -0.73060, -0.53242, -1.38074,
+ -0.15132, -0.05393, -0.08395, 0.16122, -0.51216,
+ -0.13334, 0.35404, -0.02503, -0.24533, 0.61444,
+ 1.84722, -1.52964, 0.04997, -0.90321, 1.62449,
+ -0.00456, -0.97915, 0.11311, -0.01294, -0.03718,
+ -2.34428, 0.18563, -0.80079, 2.60975, 0.07511,
+ 0.22904, 0.59156, 2.15682, 0.72828, 0.53433,
+ 1.38071, 0.14635, 0.05837, 0.09082, -0.16327,
+ 0.51244, 0.14001, -0.34669, 0.02748, 0.24661,
+ -0.61431, -1.84757, 1.52906, -0.04313, 0.90545,
+ -1.62394, -0.00019
+};
+
+float const m9_3[(na*9+1)*30+(30+1)*2] = {
+ -0.21452, -0.23367, -0.00223, 0.04134, 0.05072,
+ -0.19139, 0.04253, -0.07803, -0.17803, -0.19475,
+ -0.17788, 0.06838, 0.06174, -0.13436, 0.07630,
+ 0.03311, 0.06471, -0.12794, -0.13167, 0.04005,
+ 0.11368, 0.00126, -0.04059, -0.21324, -0.14539,
+ -0.13804, -0.01796, 0.05835, -0.08068, -0.16777,
+ 0.01824, -0.12615, -0.13140, 0.07876, 0.02766,
+ 0.07631, -0.07456, -0.13457, -0.12657, 0.08103,
+ 0.03961, 0.14463, 0.01627, -0.02288, -0.23716,
+ -0.00097, -0.12781, -0.15967, -0.15691, 0.08067,
+ 0.01602, -0.05687, 0.01944, 0.01417, -0.07269,
+ -0.08016, -0.08157, 0.10689, -0.09832, 0.10606,
+ 0.14346, -0.18050, -0.09855, -0.02273, -0.20484,
+ -0.19552, 0.02462, -0.13747, -0.22829, 0.03365,
+ 0.12683, -0.18540, -0.23596, 0.05276, 0.04894,
+ 0.05278, 0.13286, 0.08301, -0.07948, 0.07609,
+ 0.09739, -0.09032, -0.16074, -0.05928, -0.02211,
+ -0.15687, -0.16959, -0.15714, 0.07836, -0.30030,
+ -0.19507, 0.14348, 0.01470, -0.25058, -0.13015,
+ 0.08626, 0.10037, 0.09917, 0.02768, -0.12489,
+ 0.06431, 0.13969, -0.06407, -0.15175, 0.10000,
+ -0.17544, 0.00353, -0.01505, 0.02012, -0.14206,
+ -0.24851, 0.00339, 0.14234, 0.02721, -0.19548,
+ -0.15151, -0.11852, -0.17235, -0.13626, -0.11357,
+ 0.08083, -0.18543, 0.12409, -0.05128, 0.01579,
+ 0.21946, -0.19497, 0.00712, -0.18126, -0.17412,
+ 0.05841, -0.06297, -0.21101, 0.10422, -0.14424,
+ -0.15986, -0.14260, -0.09024, 0.01301, 0.07225,
+ -0.15237, 0.06736, 0.05168, -0.06987, -0.00033,
+ 0.03462, -0.09424, -0.21401, -0.16541, -0.16651,
+ -0.14928, 0.02626, -0.00336, 0.01736, 0.07102,
+ -0.17813, -0.01750, -0.16704, -0.09904, 0.00381,
+ -0.09241, -0.15096, -0.12029, 0.13399, 0.14170,
+ 0.14980, -0.19254, -0.09687, -0.19687, -0.20242,
+ -0.00985, -0.22587, -0.08781, -0.19362, 0.02766,
+ 0.07961, 0.02274, -0.16519, -0.17138, 0.02207,
+ -0.18578, -0.08933, -0.12480, -0.16513, -0.06112,
+ -0.15194, 0.07449, 0.04370, 0.29084, -0.89179,
+ -0.18310, -0.01198, -0.17063, -0.15358, -0.14321,
+ -0.05873, -0.14721, 0.08620, 0.05734, -0.15434,
+ -0.18314, -0.15992, -0.13127, -0.13909, 0.04019,
+ 0.04608, 0.03529, -0.10492, -0.11332, -0.11547,
+ 0.22531, -0.19841, -0.22260, 0.02955, 0.04573,
+ 0.05260, -0.20390, -0.12611, 0.10538, -0.15779,
+ -0.00100, 0.04142, 0.01801, -0.13830, -0.14560,
+ 0.07781, 0.12002, 0.08987, -0.16520, -0.10838,
+ 0.07141, 0.13650, -0.19597, -0.02781, -0.23670,
+ -0.15260, 0.07309, -0.00719, 0.08096, 0.09619,
+ -0.15279, -0.13896, -0.16800, 0.02806, 0.06543,
+ -0.14672, -0.14266, 0.08292, 0.09058, 0.09963,
+ -0.11799, 0.08496, 0.10658, -0.19056, -0.00561,
+ 0.00828, -0.17541, -0.11876, -0.17964, -0.14034,
+ -0.09145, 0.04069, 0.02946, -0.13802, -0.10832,
+ 0.05205, 0.06144, 0.05312, -0.12892, 0.07131,
+ 0.09586, 0.03100, -0.14482, -0.10037, 0.00767,
+ 0.02482, 0.01024, 0.04071, -0.11895, -0.22001,
+ 0.06023, 0.09523, 0.01950, 0.05808, -0.14896,
+ -0.14000, 0.09776, 0.04673, 0.01328, -0.13403,
+ -0.13112, 0.13081, -0.15283, -0.13693, -0.10000,
+ -0.19548, 0.00062, -0.23079, -0.17613, -0.15585,
+ 0.01229, -0.14397, -0.10853, 0.02340, -0.14268,
+ 0.00317, 0.06597, 0.10034, 0.09610, 0.04420,
+ -0.12375, -0.10356, 0.07310, -0.13310, 0.04361,
+ -0.02680, -0.01143, -0.01457, -0.21763, -0.14251,
+ -0.12435, -0.16391, 0.03185, -0.10093, 0.03796,
+ 0.02104, 0.00650, -0.12261, -0.08831, 0.05101,
+ -0.11632, 0.05882, 0.10113, 0.07712, -0.11200,
+ 0.04637, -0.09557, -0.20323, -0.18615, 0.00650,
+ 0.05977, 0.07654, 0.00067, 0.04822, 0.06975,
+ -0.14094, 0.03445, -0.18312, -0.11531, -0.11130,
+ 0.07136, 0.05529, 0.07949, -0.13521, -0.11286,
+ 0.06693, 0.04244, -0.10163, 0.01404, -0.15735,
+ -0.00125, 0.03972, -0.09944, -0.21217, 0.05315,
+ 0.12309, 0.03041, -0.19551, -0.21618, -0.18483,
+ 0.08495, 0.05919, 0.00397, -0.15801, -0.11518,
+ 0.07093, 0.07169, 0.10246, 0.20769, -0.88569,
+ -0.03353, -0.09324, -0.19217, 0.02653, -0.15779,
+ -0.06985, -0.17124, -0.08857, 0.04967, -0.14201,
+ 0.00717, -0.15640, 0.05953, -0.13221, 0.06879,
+ 0.07182, 0.03612, -0.09681, 0.06366, 0.08530,
+ 0.16088, -0.22974, -0.07038, 0.01399, -0.17546,
+ -0.15578, -0.02169, 0.06294, 0.14248, 0.02090,
+ -0.18892, -0.16988, -0.17299, 0.06235, -0.14515,
+ 0.08466, 0.11225, -0.07765, 0.04530, -0.08977,
+ 0.04256, 0.00648, -0.22626, -0.05993, -0.09298,
+ -0.18348, 0.07442, -0.22330, -0.12233, -0.06927,
+ -0.18386, -0.13748, 0.04309, -0.19340, -0.13030,
+ -0.12517, -0.12023, -0.08590, 0.09423, 0.12759,
+ 0.07801, 0.08722, -0.05418, -0.03939, -0.23092,
+ -0.02012, -0.00176, 0.05747, -0.01861, 0.03981,
+ 0.15597, 0.02036, 0.02920, 0.04854, 0.09498,
+ -0.13214, -0.10967, 0.06756, 0.06137, 0.08688,
+ 0.11057, 0.04756, 0.09303, -0.06421, -0.22603,
+ -0.01198, -0.03337, -0.16293, -0.11310, -0.02009,
+ 0.02894, -0.08846, -0.20835, -0.14646, -0.13139,
+ -0.13079, 0.09097, 0.05293, -0.17213, -0.11045,
+ -0.09810, 0.12566, 0.07485, -0.12100, 0.10000,
+ -0.25624, -0.24987, -0.05706, -0.00787, 0.02181,
+ -0.22278, 0.02041, -0.08251, -0.18993, 0.02298,
+ -0.17556, -0.13390, -0.08463, 0.10958, 0.08118,
+ 0.07071, 0.10593, 0.09910, 0.10783, 0.06957,
+ 0.24995, -0.21273, -0.06659, -0.04017, 0.03383,
+ -0.14099, -0.18135, -0.19913, 0.10924, 0.02779,
+ -0.12691, -0.15834, -0.13529, 0.09756, -0.11953,
+ -0.13165, 0.03058, -0.09504, 0.09873, -0.09136,
+ 0.04100, 0.15835, -0.02541, -0.20726, -0.22661,
+ -0.16197, -0.13744, 0.02757, 0.01414, 0.07070,
+ 0.03070, 0.01331, -0.16504, 0.06047, 0.06706,
+ 0.06567, -0.13809, -0.10840, -0.11103, -0.09725,
+ 0.09548, 0.07773, 0.15369, -0.01333, -0.18864,
+ -0.00458, 0.00157, -0.07268, -0.22761, 0.02971,
+ -0.07038, 0.00820, 0.02096, -0.02922, 0.00480,
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+ -0.14732, -0.26567, -0.12840, -0.05768, -0.19114,
+ -0.04751, -0.00778, -0.07861, -0.01210, -0.06641,
+ 0.22864, -0.19804, 0.04946, 0.02922, -0.17686,
+ -0.23902, -0.06963, 0.10945, -0.10739, -0.21782,
+ -0.16366, -0.00633, -0.29283, -0.12374, 0.16245,
+ -0.10387, 0.05534, 0.06612, -0.20314, 0.03931,
+ 0.10600, 0.10022, -0.22722, 0.02365, -0.08358,
+ 0.06294, -0.02158, 0.06159, -0.08738, -0.10554,
+ 0.10546, -0.00659, -0.15209, -0.51223, -0.81058,
+ -0.26313, -0.02829, -0.05898, -0.17677, -0.25332,
+ 0.18524, -0.13808, -0.09138, -0.04613, -0.05625,
+ 0.14008, 0.18868, 0.00342, 0.06680, 0.14711,
+ -0.36599, 0.10051, -0.25484, 0.09784, -0.09777,
+ 0.20046, -0.37977, -0.08626, -0.11550, 0.02214,
+ 0.02187, -0.02940, -0.12312, 0.18362, -0.37837,
+ -0.10660, -0.06417, -0.03355, 0.08974, 0.01326,
+ 0.29421, 0.08215, -0.17288, 0.04594, -0.21534,
+ -0.03570, 0.08857, 0.01426, -0.33428, 0.09862,
+ -0.15073, -0.17160, -0.47909, -0.19305, -0.03701,
+ -0.24986, -0.17929, 0.09751, -0.01337, 0.26854,
+ 0.21104, 0.30638, -0.01380, -0.17150, -0.18584,
+ 0.18224, -0.33210, 0.03376, -0.23118, -0.29141,
+ -0.08367, 0.06859, -0.15709, -0.15701, 0.02782,
+ 0.14498, -0.45873, 0.02047, -0.32312, 0.13381,
+ -0.27860, 0.34966, 0.21666, -0.22462, 0.05132,
+ 0.14181, 0.27276, -0.10858, -0.01302, -0.35477,
+ -0.12092, 0.18950, 0.12178, 0.04757, -0.13932,
+ -0.06473, 0.19624, -0.28450, 0.02369, -0.22954,
+ -0.06092, -0.04069, 0.11704, 0.12935, -0.30468,
+ 0.01907, -0.00726, 0.05139, -0.08158, 0.10000,
+ -0.04721, -0.48658, 0.16706, -0.08270, -0.14532,
+ -0.32772, -0.33208, 0.04228, -0.11415, 0.11889,
+ 0.09558, -0.16118, -0.21999, -0.36469, 0.12918,
+ -0.07989, 0.02778, 0.29551, -0.07814, -0.20771,
+ 0.27751, 0.00842, -0.11652, -0.38603, -0.17907,
+ -0.15448, -0.45002, -0.31490, -0.19035, -0.04712,
+ 0.24472, -0.18109, -0.04059, -0.14207, 0.15372,
+ 0.04544, -0.15576, -0.05947, 0.10408, 0.23805,
+ 0.26551, -0.13734, -0.01482, -0.33906, -0.11178,
+ 0.05111, -0.24121, -0.27395, -0.24656, 0.05812,
+ -0.08174, -0.11968, -0.04477, -0.04923, -0.37812,
+ 0.25889, -0.16943, -0.06585, 0.01794, 0.05624,
+ 0.26676, 0.06752, -0.13527, 0.02036, -0.24684,
+ -0.04703, -0.23560, -0.07242, 0.07075, -0.05539,
+ -0.08769, 0.14285, -0.13641, -0.04487, -0.04013,
+ -0.09502, -0.24156, 0.26934, -0.30126, 0.02775,
+ 0.04427, -0.16004, -0.28292, 0.37597, -1.14580,
+ 0.03645, -0.90934, 0.11340, -0.15178, -0.37527,
+ -1.25327, -0.81464, 0.57680, -0.48429, -0.45763,
+ -0.08670, -0.40338, -0.75128, 0.13501, 1.17841,
+ 0.02613, 0.40470, 0.43027, 0.50812, -0.17114,
+ 1.09959, -0.40065, -0.10346, 0.21044, -0.35983,
+ -0.62521, -1.03417, -0.52421, -0.14989, -0.72174,
+ -0.19528, -0.36751, 0.39206, -0.38385, 0.44133,
+ 0.76086, -0.35487, 0.94113, -0.08449, 1.01647,
+ -0.54100, 0.33697, -0.42421, -0.97280, 0.12498,
+ -0.24418, -0.23108, -0.05023, -0.48033, -0.00983,
+ 0.09262, -0.17981, -0.50500, 0.67218, -0.78304,
+ -0.05828, 0.26570, 0.13296, 0.85965, -0.05345,
+ 0.69621, -0.05508, 0.25614, -0.86972, -1.52936,
+ 0.04331, -0.34136, 0.45250, -0.52443, 0.17861,
+ -0.26997, 0.08716, 0.63037, 0.01458, 0.04554,
+ -0.31987, -0.46206, 0.67091, 0.00274, 0.64976,
+ -0.33161, 0.33831, -0.21463, 0.20233, -0.56453,
+ -1.09082, -0.70907, -0.32428, 0.50643, -1.09013,
+ 0.20231, -0.40001, -0.00636, 0.45671, -0.11809,
+ 0.00550, 0.18596, 0.15683, 0.49780, 0.82663,
+ 0.33736, -0.51223, 0.33419, 0.47646, 0.10000,
+ -1.06557, -0.81421, -0.21565, 0.08546, -0.17943,
+ -0.90927, 0.17081, -0.77807, -0.16401, -0.46597,
+ 0.13174, -0.03725, 0.89908, 0.52120, -0.02781,
+ 1.18637, 0.26897, -0.31665, 0.68847, -0.12527,
+ 0.61662, -1.09041, -1.24661, -0.08330, -0.43079,
+ -0.23906, -0.40227, 0.61972, -0.82819, -0.01363,
+ -0.78789, 0.53015, 0.45157, 1.26042, -0.10093,
+ 0.88369, 0.61920, 0.15304, 0.06336, -0.19576,
+ -0.05700, 0.16194, -0.40427, -0.86224, -0.25142,
+ -0.38139, -0.53881, -0.14171, 0.16735, -0.68536,
+ 0.28109, -0.23407, 0.19874, 0.02799, 0.31322,
+ -0.13556, 0.97874, 0.95039, -0.21109, -0.17709,
+ -0.01523, -0.12042, 0.30838, 0.12654, -1.01462,
+ 0.24325, -0.59693, 0.21201, -0.25594, 0.13122,
+ -0.76635, -1.19203, -0.30097, 0.01092, -0.02937,
+ 0.14219, -0.26131, 0.55784, 0.97519, -0.39574,
+ -0.32662, 0.59377, -0.43459, 0.84675, -1.46770,
+ 0.40084, 0.05803, -0.31249, 0.13620, -0.22692,
+ -0.17929, 0.16045, 0.59260, 0.12116, -0.12508,
+ -0.03792, 0.06010, -0.40352, -0.42494, -0.00363,
+ -0.39300, -0.05644, -0.54803, 0.25441, -0.10249,
+ -0.70691, 0.14103, -0.44679, 0.32751, 0.28034,
+ 0.19279, -0.69232, -0.31929, -0.60898, -0.60191,
+ 0.27794, -0.09604, -0.14719, 0.04323, -0.39482,
+ 0.61018, -0.00263, 0.01487, 0.08569, -0.30271,
+ 0.44769, -0.34730, 0.25616, -0.10164, 0.26844,
+ -0.28602, -0.11078, 0.53482, 0.08402, -0.13380,
+ 0.06724, -0.45987, 0.26660, 0.19297, -0.96006,
+ -0.19822, -0.56943, -0.23536, -0.24556, -0.33196,
+ 0.16361, -0.04727, -0.09258, 0.35340, 0.23082,
+ -0.46169, 0.27465, -0.10315, -0.00724, 0.16273,
+ -0.33215, 0.24462, 0.15235, -0.78161, 0.00802,
+ 0.25873, 0.36690, 0.27499, 0.22264, -0.01889,
+ -0.64984, 0.07018, -1.00601, -0.19814, -0.17246,
+ 0.27208, 0.48054, 0.20479, 0.24483, -0.53522,
+ 0.37543, 0.04712, -0.03259, 0.57660, 0.18314,
+ 0.14868, -0.09239, -0.75432, -0.48413, -0.44383,
+ 0.03401, -0.18164, -0.76942, 0.05376, 0.10000,
+ 0.00236, 0.20322, -0.12643, 0.07695, 0.39618,
+ -0.00128, -0.05895, -0.27799, -0.07757, -0.36282,
+ -0.09973, -0.16071, -0.12634, -0.33723, 0.37992,
+ 0.43214, -0.59171, -0.51553, -0.02653, -0.22349,
+ -0.24893, 0.03808, -0.21705, 0.27132, 0.14502,
+ 0.33497, -0.06347, 0.02796, -0.19983, 0.17578,
+ -0.33794, 0.62163, 0.10286, -0.30240, -0.61881,
+ -0.58116, -0.59702, 0.26325, -0.19091, 0.09767,
+ 0.13584, -0.04867, 0.00907, 0.38508, -0.39901,
+ 0.31963, 0.50932, -0.55768, -0.00563, 0.18950,
+ 0.07281, -0.80936, 0.04575, -0.50303, 0.10084,
+ -0.23082, 0.02705, 0.41085, -1.02151, -0.13331,
+ -0.35564, 0.06952, -0.06634, -0.31833, 0.36882,
+ 0.35351, -0.07205, -0.64287, -0.70301, 0.46748,
+ -0.08533, -0.31990, 0.54161, -0.15544, 0.16925,
+ -0.25420, -0.06665, 0.25863, -0.27444, -0.32051,
+ 0.31301, -0.45502, 0.04473, -0.59109, -1.25725,
+ -0.17408, -0.17529, 0.01662, 0.06746, 0.06974,
+ 0.05997, 0.06265, -0.12742, -0.13558, 0.02828,
+ 0.06396, -0.13999, 0.07466, -0.12951, 0.07540,
+ 0.03731, -0.19166, 0.08094, 0.05829, 0.03312,
+ 0.18158, -0.18172, -0.17035, -0.16427, 0.06021,
+ 0.05946, 0.05276, 0.07459, -0.11130, -0.14356,
+ 0.04879, -0.08781, -0.14713, 0.06994, 0.03595,
+ 0.07084, -0.16516, -0.16297, -0.10006, 0.04717,
+ -0.14498, -0.10347, 0.03530, -0.17876, -0.12771,
+ 0.05693, 0.07361, -0.15354, 0.05921, -0.10492,
+ 0.04505, 0.01258, -0.13702, 0.04559, -0.10721,
+ -0.09970, -0.12506, -0.14697, 0.03042, 0.06628,
+ 0.09592, 0.01451, -0.11760, -0.19158, -0.17182,
+ 0.06574, 0.06143, 0.04899, -0.20437, -0.14950,
+ -0.11286, -0.17891, 0.00162, 0.05905, 0.05461,
+ -0.12656, 0.10658, -0.10425, 0.05146, 0.03572,
+ -0.09653, 0.09277, -0.11830, 0.11361, -0.16769,
+ -0.16052, 0.01904, 0.07857, -0.14045, -0.14471,
+ 0.03516, -0.08874, -0.13658, 0.01379, -0.14474,
+ 0.06573, 0.09104, 0.05533, -0.14137, -0.16940,
+ -0.16985, -0.11197, -0.12168, -0.12234, -0.10000,
+ 0.05138, -0.19369, 0.03133, -0.14811, 0.05069,
+ -0.13451, -0.14718, 0.09315, 0.03739, -0.14550,
+ -0.13600, 0.05728, -0.16933, 0.03187, -0.07267,
+ -0.14754, -0.19091, 0.10414, -0.13213, 0.04838,
+ -0.04948, 0.04508, 0.02335, -0.17707, -0.12703,
+ -0.11949, 0.00542, -0.16914, 0.05910, -0.13292,
+ 0.08726, -0.12263, -0.12655, 0.03787, 0.09218,
+ 0.06178, -0.16894, 0.02603, 0.08165, 0.10701,
+ 0.06774, -0.11257, -0.14831, -0.15615, 0.02840,
+ -0.12125, -0.14720, -0.15298, 0.03908, -0.14831,
+ 0.02760, 0.00327, -0.16714, -0.11915, 0.03712,
+ -0.11989, -0.11333, -0.14259, -0.10351, 0.07884,
+ 0.09575, -0.11724, 0.08513, -0.12272, 0.03140,
+ 0.00949, 0.04365, -0.10570, -0.17155, -0.14273,
+ -0.15499, -0.13343, -0.08668, 0.04526, -0.12072,
+ 0.04990, 0.06316, 0.08331, -0.19646, -0.13217,
+ -0.15629, -0.14295, 0.00111, -0.02304, -0.97540,
+ 0.40357, 0.35020, -0.32883, -0.03353, 0.01023,
+ -0.17001, 0.11553, -0.08120, 0.05309, 0.14878,
+ -0.60373, -0.18122, -0.04835, -0.05499, 0.06691,
+ 0.08776, -0.22308, -0.31002, 0.17506, 0.30087,
+ -0.60649, -0.09240, 0.12460, 0.39820, 0.05701,
+ -0.07289, -0.40647, 0.22077, 0.49257, -0.03570,
+ -0.41362, -0.08308, -0.15505, -0.09328, -0.48950,
+ 0.22794, -0.16412, 0.19649, -0.66549, -0.04974,
+ 0.04490, -0.17240, -0.20116, -0.15222, 0.07443,
+ 0.15959, 0.12051, -0.24758, 0.04051, -0.11963,
+ 0.04910, 0.39345, 0.24250, 0.10353, -0.20845,
+ -0.04556, 0.06601, -0.31517, -0.01397, -0.13931,
+ -0.52629, -0.05216, 0.04062, 0.18419, 0.08351,
+ -0.17043, 0.17139, 0.06025, 0.14342, -0.07436,
+ -0.19860, 0.34876, -0.29777, 0.41515, 0.25162,
+ -0.11805, -0.04639, -0.50578, -0.55483, 0.18029,
+ -0.37514, -0.41154, -0.37226, -0.04470, -0.29246,
+ 0.29682, 0.10276, 0.28011, -0.06576, -0.03024,
+ 0.21063, -0.40430, 0.16219, 0.51398, -0.31929,
+ 0.16694, -0.02449, -0.54443, -0.00389, 0.09214,
+ -0.15004, -0.42551, -0.10839, -0.69394, -0.10000,
+ 0.00395, 0.01958, 0.03303, -0.05042, -0.10981,
+ -0.57774, 0.18361, -0.25421, 0.15639, 0.25489,
+ 0.14220, 0.18989, -0.11411, -0.22287, 0.06245,
+ -0.23689, -0.10176, -0.33273, -0.40610, -0.16712,
+ -0.40885, 0.11379, 0.15386, -0.28666, -0.04602,
+ 0.24315, 0.24819, 0.36256, 0.12718, 0.40541,
+ -0.62815, -0.27995, 0.00834, 0.18826, -0.43838,
+ 0.15154, 0.16479, -0.70498, -0.42131, -0.10814,
+ -0.16571, -0.02292, -0.15404, 0.29220, -0.03397,
+ 0.12079, 0.46750, -0.27625, -0.01122, -0.03876,
+ 0.30280, -0.22628, -0.08533, -0.19447, -0.29698,
+ -0.70475, -0.09816, -0.26862, -0.00901, -0.04486,
+ 0.05696, 0.39920, -0.13187, -0.08008, 0.07123,
+ 0.06384, 0.45493, 0.10485, -0.46200, 0.07216,
+ 0.13099, -0.27585, -0.32530, 0.02299, -0.31228,
+ -0.19736, -0.14140, 0.32250, 0.27100, -0.56588,
+ 0.04512, -0.02248, 0.19272, -0.50383, -1.06332,
+ 0.31171, 0.40084, -0.68520, -0.11016, -0.22989,
+ -0.64157, -0.07060, -0.50082, -0.14957, 0.12317,
+ -0.86955, 0.57652, 0.25906, 0.07754, -0.54701,
+ 0.61022, -0.29913, -0.05500, -0.11735, 0.52377,
+ 0.64406, -0.10273, -0.14807, -0.74087, -0.33683,
+ -0.24958, 0.42260, 0.16410, 0.00003, 0.51147,
+ -0.76219, -0.06922, -0.78905, 0.42902, -0.47389,
+ -0.09882, 0.03702, -0.02673, -0.03386, 0.07790,
+ 0.63772, -0.19473, 0.11811, 0.48663, -1.03974,
+ -0.39624, -0.40690, -0.63991, 0.23413, 0.04420,
+ 0.05750, -0.09698, 0.33727, -0.18675, 0.13946,
+ -0.11700, 0.02093, 0.45344, -0.43511, 0.36290,
+ -0.07758, -0.07512, -0.12994, 0.26946, -0.24319,
+ -0.41702, -0.59535, 0.00928, -0.48557, 0.30755,
+ 0.27739, 0.17665, -1.09215, -0.58207, 0.00446,
+ 0.62315, -0.01652, -0.76115, 1.12924, -0.37125,
+ -0.20169, 0.33098, 0.10084, 0.19026, -0.19802,
+ 0.10522, -0.00818, -0.12850, 0.57678, -0.86789,
+ -0.45180, 0.03052, -0.40161, -1.01700, -0.04585,
+ -0.03382, 0.41637, -0.51388, -0.52704, 0.79341,
+ 0.24093, 0.55541, 0.17790, -0.53633, 0.10000,
+ 0.01175, 0.52868, -0.74207, -0.54663, 0.28275,
+ 0.16603, -0.12767, 0.83528, 0.55056, -0.85762,
+ -0.31827, -0.08888, 0.50112, -0.32528, -1.18281,
+ 0.39218, -0.29657, 0.12148, -0.34381, -0.19839,
+ 0.30397, 0.06535, 0.08368, -0.37471, -0.58976,
+ 0.04077, -1.01973, -0.34575, 0.99371, 0.06498,
+ -0.35341, -0.41201, -0.42204, -0.66567, -0.48710,
+ -0.00782, 0.07665, 0.75116, 0.72744, 0.18002,
+ -0.34080, 0.09885, -0.42487, 0.41096, -0.30566,
+ -0.41636, 0.50317, -0.32376, 0.03250, 0.64115,
+ -0.72444, -0.90488, 0.15560, -0.04028, -0.41144,
+ 0.49171, -0.43964, -0.06544, 0.08252, -0.18236,
+ -0.18267, 0.04873, -0.08074, -0.91934, 0.71378,
+ 0.13155, -0.18139, -0.37435, -1.10310, -0.37457,
+ 0.39975, 0.19492, -0.07195, 0.09043, -0.54428,
+ -0.47144, -0.46121, -0.50779, -0.11381, 0.60340,
+ 0.16757, 0.09481, 0.02396, 0.76533, -1.65165,
+ -0.04715, -0.24423, -0.19559, 0.02336, 2.74814,
+ -0.00819, 0.86168, -2.50801, -0.19818, -0.29372,
+ -1.35563, -1.04514, -0.61242, -0.41749, -0.26436,
+ -0.06073, 0.07452, -0.03776, -0.03871, -0.32050,
+ -0.23739, 0.83455, 0.26672, -0.10986, 0.54688,
+ 1.73812, -1.59797, 0.07744, -1.09687, 1.97939,
+ 0.10465, 0.03987, 0.23935, 0.19678, -0.02017,
+ -2.74671, 0.00639, -0.85954, 2.50567, 0.19767,
+ 0.29963, 1.35411, 1.04420, 0.61190, 0.41814,
+ 0.26481, 0.05556, -0.07123, 0.04470, 0.03786,
+ 0.32076, 0.24292, -0.83032, -0.26635, 0.11222,
+ -0.54751, -1.73760, 1.59646, -0.07332, 1.09649,
+ -1.97761, -0.10767
+};
+
+float const m9_4[(na*9+1)*30+(30+1)*2] = {
+ -0.10197, -0.22126, 0.07820, 0.02781, 0.02423,
+ -0.07733, 0.08087, -0.13827, -0.20534, -0.25226,
+ -0.02480, 0.10267, 0.05492, -0.21829, 0.16627,
+ 0.04347, -0.04365, -0.10856, -0.35829, -0.02031,
+ 0.04681, 0.10708, 0.04860, -0.24088, -0.10384,
+ -0.21918, 0.01039, 0.06294, -0.16017, -0.20251,
+ 0.02616, -0.03199, -0.21039, 0.03854, 0.09759,
+ 0.01320, -0.13596, -0.25223, -0.11279, 0.14303,
+ 0.09389, 0.08428, 0.16258, 0.19558, -0.09526,
+ -0.10769, -0.14103, -0.06010, -0.10568, -0.00697,
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+ -0.15476, -0.11883, 0.02730, 0.01174, -0.99185,
+ 0.36958, 0.13851, -0.27128, -0.01343, 0.02518,
+ -0.16150, 0.19962, -0.15156, 0.10970, 0.27431,
+ -0.39570, -0.08519, -0.05982, -0.01499, 0.06959,
+ 0.26621, -0.17419, -0.44913, 0.16705, 0.03132,
+ -0.74552, -0.05537, 0.36518, 0.27484, -0.05762,
+ -0.16770, -0.16097, 0.15171, 0.37841, -0.01072,
+ -0.11000, -0.28883, -0.13442, 0.03953, -0.59940,
+ 0.44308, -0.07218, -0.07254, -0.36892, -0.17569,
+ -0.18492, -0.26637, -0.07391, -0.09660, -0.10143,
+ 0.21985, 0.19349, -0.32895, 0.03398, 0.00769,
+ 0.09458, 0.18523, 0.12754, 0.23811, -0.26724,
+ -0.10650, 0.14987, -0.38555, 0.17602, -0.03663,
+ -0.66571, -0.09586, 0.05912, 0.26961, -0.02726,
+ -0.05834, 0.31177, 0.18415, 0.01463, -0.09210,
+ -0.14142, 0.28040, -0.49904, 0.06410, 0.14989,
+ -0.28385, 0.03687, -0.15902, -0.39120, 0.12238,
+ -0.28945, -0.34542, -0.37865, -0.04099, -0.18113,
+ -0.07333, 0.13942, 0.35304, -0.20211, 0.15273,
+ 0.17088, -0.12733, 0.11536, 0.36907, -0.45591,
+ 0.19368, -0.22464, -0.44758, -0.02705, 0.09667,
+ 0.07979, -0.48982, -0.04228, -0.57175, -0.10000,
+ 0.00234, -0.06844, -0.03441, -0.02006, -0.11605,
+ -0.49381, -0.00588, -0.05494, 0.23464, 0.17360,
+ 0.13672, 0.09003, 0.16674, -0.15275, 0.18810,
+ -0.17339, -0.42514, -0.14608, -0.47544, -0.24206,
+ -0.45474, 0.04395, 0.07336, -0.33797, -0.04801,
+ 0.06891, 0.19878, 0.28105, 0.17208, 0.17161,
+ -0.62122, -0.16515, 0.23205, 0.09510, -0.24681,
+ 0.25027, 0.19090, -0.56814, -0.27626, -0.25789,
+ -0.13793, 0.01083, 0.02141, 0.07135, -0.29150,
+ 0.02287, 0.35266, 0.07800, -0.13221, 0.01866,
+ 0.23929, -0.01288, -0.10569, -0.16368, -0.15068,
+ -0.42282, -0.24498, -0.28941, -0.00371, 0.01190,
+ -0.12296, 0.33952, -0.08564, -0.00542, -0.10088,
+ -0.04529, 0.39507, 0.08552, -0.28795, -0.05515,
+ 0.01879, -0.14682, 0.01420, -0.05427, -0.21907,
+ -0.22506, 0.17848, 0.50022, 0.05958, -0.29528,
+ -0.18086, -0.14403, 0.05275, -0.61471, -1.02888,
+ -0.03387, 0.21864, -0.51668, -0.02667, -0.44575,
+ -0.27740, 0.25130, -0.43356, -0.14363, -0.16826,
+ -0.53046, 0.53938, 0.41350, 0.26401, -0.17859,
+ 0.19089, -0.20020, 0.25384, -0.59193, 0.04761,
+ 0.83337, 0.02343, -0.58566, -0.30431, 0.05360,
+ 0.09041, 0.11979, 0.22363, -0.25734, 0.30266,
+ -0.70893, 0.61523, -0.81211, -0.07967, -0.40157,
+ 0.05884, 0.14135, -0.11117, -0.15874, 0.10543,
+ 0.14838, 0.00485, -0.13940, -0.05453, -0.25839,
+ -0.26822, -0.32745, -0.67767, 0.21370, -0.03011,
+ 0.05412, 0.28076, 0.23418, -0.11673, 0.39324,
+ 0.06519, 0.20110, -0.09401, -0.40111, 0.07785,
+ 0.12430, -0.39965, -0.00908, 0.22867, -0.38856,
+ 0.33780, -0.33834, 0.04900, -0.87221, 0.06946,
+ -0.03270, -0.28160, -1.10689, -0.19767, 0.50987,
+ 0.40018, -0.13855, -0.29657, 0.66128, 0.10046,
+ -0.30438, 0.27084, 0.10056, 0.09747, -0.16890,
+ -0.61526, 0.09786, -0.34445, 0.46373, -0.89751,
+ -0.49254, -0.01475, -0.63772, -0.46022, 0.47834,
+ -0.04185, 0.62981, -0.04641, -0.45635, 0.39873,
+ 0.38476, 0.65927, 0.06437, -0.63351, 0.10000,
+ -0.03309, 0.39264, -0.49312, -0.24656, -0.06514,
+ 0.39002, -0.23293, 0.53003, 0.35175, -0.36836,
+ -0.63788, -0.18591, -0.03261, 0.00957, -0.45500,
+ 0.14719, -0.17749, 0.13696, -0.28075, -0.47468,
+ 0.59114, 0.22175, -0.27260, -0.48652, -0.41539,
+ -0.06077, -0.38734, -0.21385, 0.55227, 0.17909,
+ -0.00578, 0.46083, -0.33343, -1.10972, -0.37905,
+ -0.08873, -0.05396, 0.48403, 0.05770, 0.21353,
+ -0.38328, 0.28584, -0.63702, 0.20879, -0.08219,
+ -0.32231, -0.01848, -0.43415, 0.15397, 0.38288,
+ -0.38349, -0.39970, 0.10724, -0.17775, 0.11953,
+ 0.22192, -0.58974, -0.70108, -0.06120, 0.12770,
+ 0.18945, 0.27927, 0.08095, -0.60941, 0.45983,
+ 0.22731, -0.00953, -0.46710, -0.93492, -0.38843,
+ -0.08572, 0.13373, 0.35377, -0.33695, -0.40040,
+ -0.30019, -0.61900, 0.17453, -0.13130, 0.31669,
+ -0.07910, -0.07243, -0.03002, 1.06281, -1.39223,
+ 0.49233, -0.34427, 0.15098, -0.00655, 2.84438,
+ -0.04303, 0.45218, -1.92696, -0.12485, -0.31650,
+ -0.79728, -1.65571, -0.69623, -0.56704, -0.55418,
+ -0.17315, 0.01301, -0.44578, 0.25261, -0.58302,
+ -0.29915, 0.93110, 0.41221, -0.48304, 0.77552,
+ 2.00570, -1.39797, 0.12342, -0.77652, 1.58557,
+ 0.00145, -0.49850, 0.33811, -0.15027, 0.00965,
+ -2.84340, 0.04178, -0.45011, 1.92480, 0.12427,
+ 0.32165, 0.79608, 1.65517, 0.69438, 0.56902,
+ 0.55496, 0.16815, -0.00943, 0.45123, -0.25392,
+ 0.58336, 0.30525, -0.92661, -0.41080, 0.48462,
+ -0.77530, -2.00608, 1.39844, -0.11648, 0.77666,
+ -1.58499, -0.00516
+};
+
+float const m9_5[(na*9+1)*30+(30+1)*2] = {
+ -0.19290, -0.19082, 0.08590, 0.06443, 0.04775,
+ -0.14806, 0.05912, -0.11307, -0.15545, -0.17339,
+ -0.09734, 0.11640, -0.00076, -0.23042, 0.09588,
+ -0.03741, 0.04407, -0.13958, -0.21165, -0.00413,
+ 0.09321, -0.04224, 0.00755, -0.18523, -0.12075,
+ -0.15004, 0.00521, 0.07167, -0.15154, -0.20150,
+ 0.02749, -0.14203, -0.19114, 0.09143, 0.10105,
+ 0.09559, -0.08829, -0.11519, -0.08381, 0.05834,
+ 0.01239, 0.11368, 0.12249, 0.09182, -0.22592,
+ -0.02885, -0.13717, -0.10985, -0.14705, 0.04621,
+ 0.01555, -0.14121, -0.01097, 0.00968, -0.05586,
+ -0.04897, -0.14012, 0.13562, -0.09527, 0.09668,
+ 0.10905, -0.25062, -0.12277, 0.02989, -0.14734,
+ -0.18870, 0.02789, -0.13225, -0.21098, 0.07402,
+ 0.08331, -0.15530, -0.25615, 0.16900, -0.01853,
+ 0.04780, 0.17125, 0.04868, -0.08686, 0.01484,
+ 0.09233, -0.13431, -0.22558, -0.09056, -0.03172,
+ -0.09267, -0.16478, -0.14646, 0.08487, -0.34070,
+ -0.14026, 0.14552, 0.04333, -0.20634, -0.13261,
+ -0.02455, 0.12222, 0.08574, 0.04359, -0.09577,
+ 0.01121, 0.12722, -0.11155, -0.16253, 0.10000,
+ -0.07507, 0.08291, 0.01166, 0.02674, -0.11431,
+ -0.31100, 0.02671, 0.10531, 0.05332, -0.28456,
+ -0.12958, -0.15015, -0.16638, -0.15503, -0.18541,
+ 0.25193, -0.29316, 0.12997, -0.06576, -0.00739,
+ 0.16254, -0.21085, 0.05094, -0.28720, -0.16357,
+ 0.09243, -0.04205, -0.14821, 0.08506, -0.13984,
+ -0.18868, -0.18057, -0.12660, 0.08080, 0.10416,
+ -0.22211, 0.12948, 0.02950, -0.04218, 0.02075,
+ 0.03312, -0.16261, -0.22487, -0.12408, -0.13122,
+ -0.13109, 0.01654, 0.07307, 0.06009, 0.10612,
+ -0.15764, -0.16669, -0.23612, -0.12734, -0.00437,
+ -0.03730, -0.10150, -0.20158, 0.12997, 0.12113,
+ 0.14442, -0.08862, -0.20825, -0.07758, -0.16197,
+ 0.08630, -0.22217, -0.07735, -0.19544, 0.06120,
+ 0.10120, 0.01434, -0.26456, -0.15223, 0.03618,
+ -0.24121, -0.13147, -0.15880, -0.16572, -0.08251,
+ -0.24316, 0.12383, 0.11186, 0.14990, -0.91465,
+ -0.17010, 0.01660, -0.16359, -0.12349, -0.12852,
+ 0.01557, -0.11228, 0.08267, 0.03600, -0.17457,
+ -0.16874, -0.15187, -0.14162, -0.13394, 0.05473,
+ 0.03375, 0.03425, -0.10957, -0.14062, -0.15044,
+ 0.14014, -0.15141, -0.17543, 0.02050, 0.06726,
+ 0.06879, -0.16454, -0.12088, 0.08698, -0.14051,
+ 0.01598, 0.04927, 0.04631, -0.13095, -0.15818,
+ 0.07141, 0.06681, 0.02935, -0.13457, -0.13616,
+ 0.06056, 0.07425, -0.16450, 0.00444, -0.16568,
+ -0.12958, 0.07362, -0.00045, 0.08852, 0.08069,
+ -0.14233, -0.16803, -0.13383, 0.04629, 0.06091,
+ -0.14458, -0.12806, 0.05970, 0.03030, 0.08724,
+ -0.14124, 0.05193, 0.07936, -0.16609, 0.03786,
+ 0.03243, -0.14191, -0.12690, -0.18038, -0.12541,
+ -0.10588, 0.02975, 0.02821, -0.16236, -0.11614,
+ 0.06300, 0.05184, 0.06239, -0.13686, 0.02171,
+ 0.08144, 0.05244, -0.14171, -0.11271, 0.04216,
+ 0.04077, 0.01832, 0.07068, -0.15063, -0.18000,
+ 0.06776, 0.08068, 0.02769, 0.01350, -0.15864,
+ -0.12921, 0.07014, 0.06428, 0.04596, -0.14161,
+ -0.16791, 0.10758, -0.13873, -0.13812, -0.10000,
+ -0.15730, 0.02771, -0.16345, -0.14522, -0.13707,
+ 0.01185, -0.13423, -0.08860, 0.03204, -0.19091,
+ 0.00459, 0.06865, 0.08512, 0.07999, 0.06888,
+ -0.15692, -0.16096, 0.07638, -0.15920, 0.05734,
+ -0.07398, 0.03128, 0.01674, -0.17863, -0.12693,
+ -0.14231, -0.18073, 0.05310, -0.08875, 0.05061,
+ 0.01204, 0.03583, -0.13458, -0.13334, 0.07010,
+ -0.12733, 0.04120, 0.04309, 0.07884, -0.13024,
+ 0.06972, -0.11532, -0.14240, -0.15027, 0.02327,
+ 0.07428, 0.06484, -0.00368, 0.06994, 0.08658,
+ -0.16653, 0.02154, -0.15239, -0.13341, -0.14211,
+ 0.05168, 0.07897, 0.04853, -0.15479, -0.12859,
+ 0.06189, 0.05839, -0.12178, 0.04126, -0.16827,
+ 0.02097, 0.06146, -0.11028, -0.17978, 0.07097,
+ 0.08937, 0.02927, -0.15160, -0.15915, -0.15757,
+ 0.05275, 0.05597, 0.03722, -0.15244, -0.14899,
+ 0.07233, 0.03942, 0.05218, 0.14885, -0.86027,
+ -0.08495, -0.05260, -0.18596, 0.04859, -0.14866,
+ -0.02615, -0.12610, -0.10342, -0.02225, -0.18464,
+ 0.03069, -0.15970, 0.05099, -0.13277, 0.09694,
+ 0.02679, 0.05595, -0.06803, 0.05874, 0.05505,
+ 0.19046, -0.21805, -0.06834, 0.00350, -0.17956,
+ -0.16912, 0.01644, 0.05615, 0.12797, -0.02009,
+ -0.20847, -0.10162, -0.14587, 0.11895, -0.14716,
+ 0.05996, 0.08805, -0.11721, 0.10405, -0.11628,
+ 0.06455, -0.02765, -0.23569, -0.05819, 0.00508,
+ -0.18567, 0.05384, -0.24521, -0.12563, -0.09127,
+ -0.22045, -0.18944, 0.08636, -0.15486, -0.07649,
+ -0.08996, -0.12045, -0.09240, 0.07129, 0.11337,
+ 0.09081, 0.05301, -0.06815, -0.04783, -0.22352,
+ -0.00091, 0.00101, 0.03782, -0.03396, 0.04329,
+ 0.15485, -0.01044, 0.01234, 0.08700, 0.03957,
+ -0.08702, -0.10061, 0.08586, 0.08893, 0.03443,
+ 0.12594, 0.12545, 0.06096, -0.07323, -0.23230,
+ -0.00687, -0.02246, -0.16509, -0.17493, -0.03903,
+ 0.02065, -0.05563, -0.22977, -0.19499, -0.10753,
+ -0.16067, 0.09181, 0.10559, -0.11864, -0.09709,
+ -0.12693, 0.14784, 0.11735, -0.13113, 0.10000,
+ -0.23620, -0.23611, 0.00755, -0.01460, 0.02966,
+ -0.22641, 0.00707, -0.04238, -0.23478, -0.03711,
+ -0.15748, -0.16644, -0.06492, 0.12734, 0.11418,
+ 0.06928, 0.03884, 0.12539, 0.09298, 0.08332,
+ 0.24093, -0.21202, -0.04259, -0.03904, 0.03389,
+ -0.17012, -0.23460, -0.21716, 0.14045, 0.01183,
+ -0.12808, -0.15281, -0.16437, 0.08720, -0.08282,
+ -0.11581, 0.02178, -0.12624, 0.12325, -0.05051,
+ 0.09797, 0.13878, 0.02507, -0.19659, -0.20963,
+ -0.16262, -0.15761, -0.04689, 0.03358, 0.09937,
+ -0.03544, 0.00308, -0.15188, 0.04346, 0.05265,
+ 0.07479, -0.11591, -0.14461, -0.08895, -0.10007,
+ 0.13696, 0.11797, 0.14125, 0.02230, -0.19567,
+ 0.01325, -0.00857, -0.07566, -0.20333, 0.04045,
+ -0.09968, -0.03212, 0.04306, 0.00678, 0.00327,
+ -0.13497, 0.04822, 0.01765, -0.19230, 0.08753,
+ 0.06222, -0.11801, -0.11584, 0.14939, -0.89917,
+ -0.00680, 0.03829, 0.02039, 0.08346, -0.12475,
+ -0.17086, 0.09745, 0.05494, -0.17054, 0.03760,
+ 0.07515, 0.10220, -0.12262, -0.15124, -0.16609,
+ -0.17811, 0.04717, 0.08094, 0.01562, -0.12768,
+ 0.25285, 0.01784, -0.16080, -0.14065, 0.06959,
+ 0.06052, 0.04416, -0.10160, 0.06550, -0.14539,
+ -0.16897, 0.05875, 0.02145, 0.07545, 0.09279,
+ 0.07051, 0.03931, 0.08557, 0.10900, 0.01391,
+ -0.15117, -0.06776, 0.05187, 0.05042, -0.11408,
+ -0.16035, -0.12711, -0.03238, -0.12954, -0.10489,
+ 0.01348, 0.02508, 0.04933, -0.12468, 0.12141,
+ 0.13929, 0.08997, -0.13202, -0.20829, 0.14290,
+ 0.04890, -0.02164, 0.11018, -0.20652, 0.07264,
+ 0.06688, 0.04728, 0.06766, -0.08991, 0.07150,
+ -0.12786, -0.18363, -0.05617, -0.03851, 0.03671,
+ -0.11214, -0.08305, 0.03673, 0.02261, -0.18251,
+ 0.09911, 0.09939, -0.17615, -0.07622, 0.02388,
+ 0.04448, -0.00186, 0.08480, -0.09652, -0.22562,
+ -0.13418, -0.13631, 0.03603, -0.14853, -0.09310,
+ -0.18609, -0.11744, -0.12370, -0.13069, -0.07997,
+ -0.18554, 0.11095, -0.10951, 0.05720, -0.10000,
+ 0.02890, 0.05972, -0.11639, -0.18381, 0.04384,
+ 0.00292, -0.15909, -0.12853, -0.15970, -0.18122,
+ 0.00580, 0.02771, 0.09309, 0.08437, -0.09942,
+ 0.11139, -0.12525, -0.10815, 0.09378, -0.15740,
+ -0.04461, 0.03557, 0.04805, -0.21200, -0.13106,
+ 0.07479, -0.18078, 0.03993, -0.12429, -0.15922,
+ -0.16176, 0.05717, 0.08452, 0.06411, -0.08935,
+ -0.11841, -0.10358, -0.19923, -0.09529, -0.06803,
+ -0.12795, 0.05358, 0.06031, 0.02904, -0.17237,
+ -0.15332, -0.11173, 0.08407, -0.11993, 0.03910,
+ -0.16776, -0.25106, -0.14696, -0.15130, 0.04370,
+ -0.09085, -0.16055, -0.15156, -0.11922, -0.08626,
+ -0.08445, -0.04570, -0.15711, -0.14288, -0.11358,
+ -0.00924, 0.04925, -0.02074, -0.19363, -0.15715,
+ -0.12316, -0.18999, 0.01425, -0.21176, -0.13990,
+ 0.07169, -0.12774, -0.11538, -0.18401, 0.06045,
+ -0.11614, 0.08174, 0.10404, 0.14998, -0.92986,
+ -0.70343, 0.15052, 0.10742, 0.19836, -0.08073,
+ -0.79819, 0.17687, 0.18368, 0.12656, 0.57625,
+ -0.49470, -0.46343, 0.28071, -0.06849, -0.43462,
+ -0.49867, -0.67505, 0.19501, -0.14914, -0.12151,
+ 0.36435, -0.78631, -0.00863, 0.33520, 0.35629,
+ 0.26541, -0.17393, 0.18435, 0.30149, 0.03765,
+ 0.31147, -0.60558, -0.48898, -0.19439, -0.00322,
+ 0.18783, -0.47206, -0.70685, 0.15218, -0.55910,
+ 0.53610, -0.19355, -0.87061, 0.05389, -0.25676,
+ 0.32038, -0.09087, -0.38368, 0.03088, 0.38494,
+ -0.33603, 0.45487, 0.36895, -0.54325, 0.27691,
+ -0.08895, 0.54800, -0.06829, -1.22638, 0.22665,
+ -0.00164, 0.31501, -0.03941, -0.58310, 0.16466,
+ -0.15313, -0.05756, -0.39947, -0.42991, 0.12586,
+ 0.46280, -0.27298, 0.20445, -0.47509, -0.50300,
+ 0.61751, 0.26497, 0.22209, -0.21569, -1.10737,
+ 0.64735, 0.75701, -0.30943, -0.08538, -0.32156,
+ -0.64024, 0.28231, 0.08740, 0.62053, -0.31257,
+ -0.61010, 0.22274, -0.63234, 0.19124, 0.43564,
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+ 0.50878, 0.53940, 0.04491, -0.64704, -1.81683,
+ -0.67162, -0.12981, 0.12564, -0.42601, -0.07913,
+ 0.03174, -0.35624, 1.40403, -0.14255, 0.08216,
+ -0.29909, -0.46542, 0.59075, -0.21025, 1.01924,
+ -0.39037, 0.16350, 0.45056, 0.12580, -0.51815,
+ -0.95563, -0.22205, 0.14687, -0.23931, -0.75530,
+ -0.18337, 0.37108, -0.44927, 0.89402, 0.24204,
+ 0.90138, -0.05130, -0.83553, 0.10225, -0.00735,
+ 0.81345, -0.45714, -0.21835, 0.49818, 0.10000,
+ -0.76107, -1.24544, -0.33617, 0.17968, -0.37562,
+ -0.56136, -0.02983, 0.25225, -0.18729, -0.06288,
+ 0.99677, 0.70911, -0.10613, -0.59167, -0.18363,
+ -0.09470, 0.98424, -0.01849, -0.56502, 0.06270,
+ 1.30564, -0.43758, -1.38387, -0.29249, 0.07790,
+ 0.29913, -0.48238, -0.03058, -0.08201, 0.03310,
+ 0.11188, 0.29394, 0.12218, 0.25062, -0.50525,
+ 0.61633, -0.37818, 1.02156, 0.17985, -0.40624,
+ -0.38725, 0.54057, 0.07337, -1.67657, 0.03836,
+ 0.00173, -0.27955, -0.76571, -0.54401, -0.35304,
+ 0.48506, 0.09995, 0.27571, 0.59615, -0.01635,
+ -0.20221, 0.65387, 0.85042, 0.63693, -0.06348,
+ -0.51507, -0.70176, 0.36166, -0.24087, -1.58471,
+ -0.58591, 0.36929, -0.79049, -0.42019, -0.25691,
+ -0.25110, -0.56857, -0.04524, 0.41867, 0.47787,
+ 0.16911, 0.07901, 0.75175, 0.04694, -0.10104,
+ 0.22451, -0.20654, -1.26145, 1.93132, -1.59908,
+ 0.27608, 0.23295, 0.05954, 0.23386, -0.23811,
+ -0.56604, -0.02589, 0.23298, 0.32663, -0.12709,
+ -0.82259, 0.24834, -0.64757, -0.11928, -0.20345,
+ -0.03277, 0.28468, -0.56154, 0.40509, 0.11260,
+ -0.74392, -0.00697, -0.24591, 0.19447, 0.07638,
+ 0.17388, -0.71238, -0.19964, -0.17372, -0.33703,
+ -0.02442, 0.18134, 0.27945, -0.27966, -0.21485,
+ 0.25936, -0.32309, -0.44015, 0.29614, 0.05064,
+ 0.26584, -0.29796, 0.00212, -0.05619, 0.41631,
+ -0.16623, -0.05042, 0.54889, 0.06436, 0.01081,
+ 0.25063, -0.13205, -0.00117, -0.11018, -0.90482,
+ -0.18795, -0.39939, -0.44218, -0.08857, -0.52717,
+ 0.20060, -0.29802, -0.00698, 0.19246, 0.13621,
+ -0.61288, 0.28471, -0.14381, 0.10550, 0.06541,
+ -0.24776, 0.50798, -0.10229, -0.71815, 0.03433,
+ 0.30816, 0.22213, -0.07049, 0.19780, 0.19056,
+ -0.43758, -0.02684, -0.75994, -0.00312, 0.04693,
+ 0.26368, 0.07741, 0.35669, 0.08613, -0.43279,
+ 0.34625, 0.08879, 0.02249, 0.45587, -0.20877,
+ 0.05043, -0.33844, -0.89349, -0.18701, -0.08705,
+ 0.24678, -0.23736, -0.66096, 0.22507, 0.10000,
+ 0.13648, 0.18977, 0.17950, 0.09826, 0.48805,
+ -0.03745, -0.12208, -0.06473, -0.16134, -0.60672,
+ -0.21308, 0.10152, -0.62681, -0.24374, -0.27993,
+ 0.10605, 0.24144, -0.39545, 0.17419, -0.37236,
+ -0.26953, -0.17181, 0.08495, 0.22329, 0.27891,
+ 0.20805, 0.02708, 0.00486, -0.22438, 0.21979,
+ 0.12208, 0.21123, -0.10572, -0.25216, -0.32307,
+ -0.59698, -0.34408, -0.01889, -0.24860, -0.04481,
+ 0.08254, -0.00445, 0.01850, 0.38276, 0.15915,
+ 0.10996, 0.60741, -0.44280, -0.07302, -0.10677,
+ 0.17429, -0.34208, 0.27443, -0.00618, -0.00401,
+ -0.44123, -0.17937, -0.49177, -0.83449, -0.14124,
+ -0.47550, -0.00514, -0.05153, -0.34104, 0.34460,
+ 0.57737, -0.05875, -0.69845, 0.04134, 0.28244,
+ -0.11231, 0.08808, 0.13943, -0.09535, 0.21333,
+ -0.23731, 0.06333, 0.05767, -0.45051, -0.24535,
+ 0.02958, -0.42693, -0.12088, -0.71894, -1.18298,
+ -0.17828, -0.20880, 0.06469, 0.07530, 0.07006,
+ 0.01823, 0.05945, -0.14643, -0.12409, 0.06539,
+ 0.10281, -0.13001, 0.03310, -0.15564, 0.07699,
+ 0.01921, -0.25233, 0.09526, 0.04302, 0.07023,
+ 0.21938, -0.21867, -0.15837, -0.13367, 0.07456,
+ 0.04349, 0.04800, 0.08133, -0.11420, -0.17129,
+ 0.10795, -0.06444, -0.19061, 0.11396, 0.04206,
+ 0.03167, -0.20620, -0.18218, -0.08452, 0.04887,
+ -0.15152, -0.09807, 0.06605, -0.11808, -0.12147,
+ 0.05617, 0.07462, -0.11751, 0.06618, -0.11701,
+ 0.02585, 0.03726, -0.15105, 0.01635, -0.10795,
+ -0.12427, -0.18044, -0.12353, -0.00166, 0.05851,
+ 0.10380, -0.00654, -0.11727, -0.21114, -0.21811,
+ 0.07646, 0.05981, 0.06529, -0.19556, -0.13788,
+ -0.12089, -0.19054, -0.02851, 0.11569, 0.00909,
+ -0.10462, 0.10933, -0.09876, 0.07648, 0.02610,
+ -0.09853, 0.10384, -0.12351, 0.10396, -0.19496,
+ -0.12673, -0.00741, 0.07705, -0.15926, -0.17052,
+ 0.06728, -0.09608, -0.13285, 0.00619, -0.14023,
+ 0.03056, 0.17743, 0.02459, -0.12798, -0.15314,
+ -0.17185, -0.12381, -0.17240, -0.08698, -0.10000,
+ 0.07566, -0.13235, -0.00253, -0.16354, 0.07613,
+ -0.09469, -0.12516, 0.03121, 0.01646, -0.20750,
+ -0.13041, 0.01753, -0.13604, 0.02901, -0.08261,
+ -0.07057, -0.23868, 0.10930, -0.14124, 0.05973,
+ -0.07116, 0.03493, 0.04314, -0.29295, -0.12677,
+ -0.12135, 0.05417, -0.14388, 0.02612, -0.16425,
+ 0.07168, -0.10810, -0.11118, 0.13332, 0.09186,
+ 0.06814, -0.16108, 0.00413, 0.10221, 0.13620,
+ 0.05166, -0.17045, -0.16420, -0.11867, 0.06555,
+ -0.12296, -0.14276, -0.09772, 0.06156, -0.16341,
+ 0.01670, -0.04522, -0.17676, -0.16083, 0.05637,
+ -0.14060, -0.08885, -0.19712, -0.12741, 0.07423,
+ 0.12334, -0.03435, -0.00006, -0.07692, 0.08090,
+ 0.04732, 0.02422, -0.07502, -0.18435, -0.12276,
+ -0.18210, -0.12756, -0.15359, 0.11046, -0.15358,
+ 0.05036, 0.05474, 0.06339, -0.24503, -0.17052,
+ -0.18758, -0.06372, 0.02959, -0.10144, -1.00057,
+ 0.36454, 0.44383, -0.09458, 0.03946, -0.14226,
+ -0.11572, 0.10862, -0.14234, 0.31735, 0.21923,
+ -0.34357, -0.38084, 0.06804, -0.01798, -0.15942,
+ 0.37505, -0.36748, -0.52233, 0.13506, -0.04848,
+ -0.73951, -0.33413, 0.36436, 0.15440, 0.13246,
+ -0.16216, -0.20685, 0.22388, 0.43739, 0.15948,
+ -0.27506, -0.57769, -0.23283, -0.11793, 0.04325,
+ 0.20835, -0.06387, -0.00972, -0.43239, -0.13390,
+ -0.11412, -0.26854, -0.46915, -0.14613, 0.02656,
+ 0.02371, 0.21529, -0.37052, 0.13177, -0.09088,
+ 0.08122, 0.06475, 0.25384, 0.14760, -0.18000,
+ -0.36738, -0.03720, -0.17506, 0.31111, 0.06682,
+ -0.60490, 0.27882, 0.03464, -0.01719, 0.22687,
+ -0.28128, 0.20727, 0.20833, 0.46467, -0.31582,
+ -0.21036, 0.39513, -0.09427, 0.19853, -0.03639,
+ -0.24067, -0.11015, -0.22235, -0.45964, 0.37564,
+ -0.39061, -0.65427, -0.42772, -0.02081, -0.17972,
+ 0.16637, 0.04165, 0.43486, -0.23090, 0.24861,
+ 0.16303, -0.31433, 0.09594, 0.29408, -0.50914,
+ 0.30313, -0.15168, -0.72502, -0.10152, 0.16950,
+ -0.05108, -0.58055, 0.08094, -0.46120, -0.10000,
+ 0.05044, 0.03104, 0.09317, 0.09938, 0.02575,
+ -0.46800, 0.10572, 0.00708, 0.13676, -0.08237,
+ 0.00289, 0.04881, -0.09953, -0.58966, 0.02839,
+ -0.11267, -0.24785, -0.22058, -0.29737, -0.04718,
+ -0.46954, 0.02445, 0.16066, 0.00049, -0.03265,
+ 0.12964, 0.18583, 0.38077, 0.12620, 0.29787,
+ -0.90897, -0.08752, 0.01981, -0.46549, -0.55576,
+ 0.07166, 0.08566, -0.03348, -0.39697, 0.04958,
+ -0.13116, 0.07828, -0.24735, 0.43257, -0.14998,
+ 0.12436, 0.37034, -0.18352, -0.07362, -0.25982,
+ 0.37413, -0.04181, -0.17871, -0.05747, -0.19322,
+ -0.47839, -0.31607, -0.46676, -0.15988, 0.06955,
+ 0.24653, 0.16829, 0.02282, -0.24617, 0.04788,
+ -0.01848, 0.29072, 0.01010, -0.15979, 0.01634,
+ -0.07690, 0.03149, 0.11813, -0.12768, -0.09899,
+ -0.23942, -0.14348, 0.50440, -0.09087, -0.38251,
+ 0.02048, -0.18637, -0.01891, -0.44796, -1.12600,
+ 0.40579, 0.41887, -0.61991, 0.08092, -0.68587,
+ -0.48954, -0.00298, -0.37416, -0.12532, -0.33235,
+ -0.47341, 0.46050, -0.35424, 0.29649, -0.12607,
+ 0.02370, -0.00464, 0.23501, -0.24720, 0.20501,
+ 1.04298, -0.23443, 0.05167, -0.61089, -0.07674,
+ -0.48339, 0.38459, -0.08989, 0.24743, 0.04536,
+ -0.72797, 0.23255, -0.54903, -0.37946, -0.19735,
+ 0.07823, -0.02622, -0.02599, 0.23207, 0.13901,
+ 0.25724, 0.06960, -0.03078, 0.23182, 0.09157,
+ -0.41028, -0.47918, -0.27915, 0.11317, 0.25901,
+ -0.06966, -0.30038, 0.17530, -0.15162, 0.09398,
+ 0.05675, -0.30927, -0.02397, -0.04419, 0.38141,
+ -0.00556, -0.54977, -0.01354, 0.13518, -0.13092,
+ 0.39024, -0.34537, -0.20804, -0.50064, 0.18836,
+ 0.31226, 0.03702, -0.64454, -0.23362, 0.18629,
+ -0.09089, -0.27043, -0.57803, 0.97612, 0.08897,
+ -0.20347, -0.03329, -0.33227, -0.00730, -0.35208,
+ -0.71055, -0.29380, -0.43208, 0.40704, -0.64446,
+ -0.41683, 0.26587, -0.27059, -0.45602, -0.16275,
+ -0.16872, 0.18117, -0.02179, -0.46815, 1.11857,
+ 0.49056, 0.46903, -0.19444, -0.09819, 0.10000,
+ 0.11553, 0.41152, -0.34435, -0.53958, -0.05883,
+ -0.36942, -0.34741, 0.60288, 0.16591, -0.53797,
+ -0.93248, -0.07150, 0.33389, 0.59125, -0.51544,
+ 0.19072, 0.07358, -0.01456, -0.25522, -0.09719,
+ 0.33853, -0.13148, -0.16613, -0.67831, -0.37644,
+ -0.07053, -0.69834, -0.37220, 0.38571, -0.11124,
+ -0.95893, 0.10263, -0.35191, -0.69345, 0.12528,
+ 0.16868, 0.42630, 0.67255, 0.52657, 0.27489,
+ 0.08935, -0.02929, -0.26288, 0.22561, -0.56069,
+ -0.20470, 0.08457, -0.50511, -0.16079, 0.43472,
+ -0.45525, -0.62159, -0.35162, -0.52752, -0.38190,
+ 0.46469, 0.11206, -0.37609, 0.55361, 0.06389,
+ 0.40947, 0.32307, -0.33314, -0.21198, 0.30628,
+ 0.64346, -0.22899, -0.00676, -1.07624, -0.72754,
+ 0.14441, -0.19778, -0.19886, -0.12671, -0.17085,
+ -0.29789, -0.24591, 0.05353, -0.48104, 0.10198,
+ -0.36060, 0.37146, 0.39582, 0.44465, -1.56670,
+ 0.24294, -0.12999, -0.16319, 0.17663, 1.87324,
+ -0.14988, 1.40657, -1.88775, -0.12755, -0.18664,
+ -0.86751, -1.61501, -0.48438, -0.64133, -0.53517,
+ 0.01357, -0.13414, 0.08427, 0.23994, -0.73614,
+ -0.32733, 0.19979, -0.04565, -0.42306, 0.27203,
+ 2.01338, -1.27246, 0.14468, -1.05349, 1.67586,
+ 0.04924, -0.25029, 0.12518, 0.16371, -0.17465,
+ -1.87260, 0.14771, -1.40553, 1.88657, 0.12783,
+ 0.19057, 0.86719, 1.61480, 0.48053, 0.64192,
+ 0.53691, -0.01862, 0.13578, -0.07692, -0.24021,
+ 0.73644, 0.33234, -0.19241, 0.04762, 0.42418,
+ -0.27139, -2.01344, 1.27309, -0.13775, 1.05439,
+ -1.67483, -0.05316
+};
+
+float const m21_1[(na*21+1)*30+(30+1)*2] = {
+ 0.04166, -0.83383, 0.26526, -0.03265, -0.01552,
+ -0.54619, 0.18081, -0.05454, -0.25178, -0.06791,
+ -0.23795, -0.11350, -0.32602, -0.18666, 0.19567,
+ -0.07327, 0.94547, -0.22610, 0.05460, -0.38648,
+ -0.25391, 0.33291, -0.04810, 0.08243, -0.55076,
+ -0.19572, -0.42399, 0.50229, 0.12340, 0.50488,
+ 0.15321, 0.52714, -0.27336, 0.09493, -0.24109,
+ 0.54114, -0.54449, -0.75175, -0.97297, -0.49090,
+ -0.08315, -0.00889, -0.08170, 0.69857, -0.28045,
+ 0.21507, 0.04344, -0.44751, -0.08549, -0.36361,
+ -0.10833, 0.18763, -0.07888, -0.08886, -0.13733,
+ -0.96481, -0.84890, 0.65271, -0.00346, 0.19603,
+ -0.31151, 0.59388, -0.50930, 0.41489, -0.66201,
+ -0.37182, -0.17664, -0.14911, -0.41892, -0.39120,
+ -0.03086, -0.28801, -0.24257, 0.94960, 0.49527,
+ 0.03001, 0.90337, -0.01208, 0.09802, 0.24738,
+ -0.93347, -0.27480, -0.26670, -0.64318, -0.77049,
+ 0.46420, -0.56184, 0.01963, 0.30966, -1.30839,
+ -0.45513, 0.11736, 0.25014, -0.44313, 0.25962,
+ 0.02389, -0.34815, 0.32183, 0.38427, 0.19955,
+ 0.37937, -0.24922, 0.07544, -0.18204, -0.20942,
+ -0.17251, -0.23633, 0.26875, 0.40686, 0.18379,
+ -1.12242, 0.07428, -0.77180, -0.02175, 0.54820,
+ 0.33146, -0.15174, -0.39398, -0.34706, 0.39797,
+ -0.10149, -0.95320, 0.05601, 0.50218, -0.35230,
+ -0.06776, -0.58304, 0.06003, -0.09281, -0.46911,
+ 0.22378, -0.12788, -0.35196, -0.25114, -0.97052,
+ -0.41803, 0.06794, -0.10105, -0.00087, 0.00009,
+ -0.74702, 0.46545, 0.71040, 0.23410, 0.17202,
+ 0.24560, -0.18883, -0.10129, -0.12048, -0.79415,
+ -0.05009, -0.07034, -0.48541, -0.46079, 0.54457,
+ -0.10030, 0.93304, -0.94218, -0.29347, 0.33843,
+ 0.25945, -0.83633, 0.31163, 0.00805, 0.60433,
+ 0.14106, -0.91058, -0.09798, 0.37040, -0.89724,
+ -0.04220, -0.92170, -0.24053, 0.32045, -0.50161,
+ 0.55363, 0.24428, 0.19014, -0.48619, -0.47371,
+ -0.73740, -0.14947, -0.26186, -0.06140, 0.75107,
+ 0.03653, 0.50369, -0.60644, 0.08674, -0.07757,
+ -0.48128, -0.55770, -0.32147, -0.68124, -0.31905,
+ -0.51296, 0.19572, 0.52891, 0.65091, 0.25138,
+ 0.07580, -0.49723, -0.80185, 0.14727, 0.23630,
+ -0.32673, 0.03671, -0.59474, 0.66149, 0.06447,
+ 0.15008, -0.56910, 0.22000, -0.08110, -0.66611,
+ -0.35942, -0.24623, -0.50948, 0.44740, -0.05952,
+ -0.43452, 0.53496, 0.63065, -0.37490, -0.57731,
+ 0.28008, 0.25166, -0.04412, -0.59056, 0.37470,
+ 0.10000, -0.26996, -0.90792, 0.05223, -0.10863,
+ -0.35339, -0.25186, 0.34514, -0.17248, 0.62290,
+ 0.28417, 0.36548, -0.34938, 0.42219, -0.44713,
+ 0.06974, 0.19532, -0.22224, -0.25098, -0.61560,
+ -0.27038, 0.33995, -0.39560, -1.48108, -0.59837,
+ -0.27362, 0.28083, 0.05023, -0.07839, -0.24436,
+ 0.17242, -0.00499, 0.39253, 0.31952, -0.05708,
+ 0.16695, 0.08823, -0.01544, 0.35403, 0.14735,
+ -0.20277, -0.12933, -0.21390, -1.31706, -0.15756,
+ -0.11622, -0.01507, -0.44364, -0.65832, -0.98477,
+ -0.67705, -0.55408, 0.03722, 0.08818, -0.07082,
+ -0.23406, -0.03568, 1.03132, 0.79799, 0.93014,
+ -0.22240, 0.76866, 0.17498, 0.13541, -0.42975,
+ 0.05005, 0.27662, 0.10925, -0.72800, -0.27439,
+ -0.29074, -0.10894, -0.44856, -0.73320, 0.34244,
+ -0.36985, 0.12089, 0.54410, -0.09826, 0.20938,
+ 0.20256, -0.13137, -0.10771, -0.44429, 0.38693,
+ -0.94424, 1.02512, 0.39544, -0.07556, -0.60373,
+ -0.44643, -0.39157, -0.48191, 0.20341, 0.16395,
+ 0.10259, 0.50572, -0.34254, -0.59622, -0.47490,
+ -0.10470, 0.19796, 0.23906, 0.06044, -0.32982,
+ 0.17508, 0.11531, -0.75065, 0.16163, 0.05608,
+ 0.57665, -0.13467, 0.12456, 0.01782, 0.16388,
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+ -0.22405, 0.07539, -0.18784, 0.01928, 0.20705,
+ -0.19115, 0.11708, -0.20164, -0.22791, 0.03355,
+ 0.15189, -0.01644, -0.00876, 0.09180, 0.09750,
+ 0.13963, 0.01516, 0.02254, 0.02097, 0.03066,
+ 0.01515, -0.09507, 0.13711, -0.08033, -0.14479,
+ -0.03993, 0.04897, 0.21293, -0.26278, -0.24392,
+ 0.06091, -0.01220, 0.01742, 0.04788, -0.10338,
+ 0.05328, 0.06539, -0.19683, 0.05265, 0.02513,
+ -0.07761, -0.08899, 0.09422, -0.14080, -0.06746,
+ -0.01495, 0.18842, -0.17192, 0.25273, -0.19812,
+ -0.18077, 0.07973, -0.16061, -0.18779, -0.05370,
+ -0.19952, 0.02604, -0.08170, 0.07546, 0.11048,
+ -0.23971, 0.08037, -0.06442, -0.14863, 0.00789,
+ -0.14166, 0.02700, 0.00918, 0.10854, 0.06398,
+ 0.01167, -0.18927, 0.22368, 0.04565, -0.15297,
+ -0.11671, -0.26275, 0.10466, -0.08416, 0.04939,
+ -0.10207, -0.16721, -0.13724, -0.13637, -0.01612,
+ 0.02409, 0.07108, -0.12369, -0.06075, 0.05049,
+ -0.05702, -0.02088, -0.15680, 0.03233, -0.16025,
+ 0.04145, -0.09105, 0.02588, 0.05628, 0.12069,
+ 0.09691, 0.06226, -0.17208, -0.05968, -0.00420,
+ -0.08432, -0.17541, -0.21310, 0.12035, 0.11402,
+ 0.02418, -0.04538, 0.00978, -0.24351, 0.02520,
+ -0.12842, 0.06271, 0.09800, -0.00719, 0.02083,
+ -0.03249, 0.00468, -0.02731, -0.17298, -0.13625,
+ -0.13618, 0.09216, 0.02827, -0.06227, -0.02631,
+ 0.17143, -0.22327, 0.13469, 0.10005, 0.12355,
+ -0.04922, -0.11064, 0.01577, 0.07717, -0.10054,
+ -0.14613, 0.09724, -0.01552, 0.05517, -0.03556,
+ 0.15592, -0.04035, 0.04663, -0.23723, -0.15170,
+ 0.08465, 0.16069, 0.03414, 0.12103, 0.05677,
+ -0.65817, -0.09739, 0.11666, 0.09813, -0.13384,
+ -0.05076, -0.10632, -0.11780, -0.07037, -0.02007,
+ -0.19340, -0.17155, -0.08588, 0.03609, 0.16445,
+ 0.03594, -0.13463, -0.18669, 0.04157, -0.19912,
+ -0.03041, -0.08964, -0.04830, -0.04814, 0.07942,
+ -0.12957, -0.07502, -0.05963, 0.01968, 0.12499,
+ -0.05338, 0.11910, -0.09293, 0.02493, 0.03234,
+ 0.07801, -0.14198, -0.00392, -0.04027, 0.03697,
+ -0.17448, -0.02346, -0.01941, 0.17518, -0.11950,
+ -0.01354, -0.10847, -0.09148, 0.01278, -0.16531,
+ 0.09988, -0.02837, -0.16817, 0.11159, -0.03368,
+ -0.03011, 0.05332, 0.00977, -0.16021, -0.02288,
+ -0.15020, 0.03220, -0.22758, -0.17022, 0.21767,
+ -0.02283, 0.01224, 0.13048, -0.12271, -0.09575,
+ 0.01561, -0.09710, -0.00239, -0.11401, -0.20100,
+ -0.05784, -0.28981, 0.08463, -0.13878, 0.05549,
+ 0.02226, -0.20686, -0.07234, -0.15769, -0.15430,
+ 0.05333, -0.06664, -0.11102, -0.10483, -0.07202,
+ 0.25761, -0.13870, -0.17243, -0.01943, -0.04637,
+ 0.05098, 0.05462, -0.20200, 0.04267, 0.01612,
+ 0.02678, -0.15075, -0.17363, -0.10381, 0.00235,
+ -0.13786, -0.02312, -0.11220, -0.11102, 0.12188,
+ 0.14067, 0.02159, 0.08127, -0.02130, 0.16722,
+ 0.05648, 0.08541, -0.03311, -0.03012, -0.12966,
+ -0.02693, 0.04875, -0.01817, -0.13639, -0.25086,
+ -0.23819, 0.01279, 0.22384, 0.00587, 0.04902,
+ 0.10872, -0.09834, 0.19064, 0.11836, -0.14083,
+ 0.16729, -0.27617, -0.14939, 0.15772, -0.19121,
+ -0.21430, -0.18106, 0.01846, -0.17320, 0.01658,
+ -0.02984, -0.22630, -0.17091, 0.01391, 0.04411,
+ 0.05676, 0.11807, 0.08725, 0.05513, 0.13789,
+ -0.02584, -0.04202, -0.26178, -0.13867, -0.08890,
+ -0.17769, 0.07908, 0.03585, 0.02168, 0.05622,
+ -0.17239, -0.19490, -0.25747, -0.14129, 0.16276,
+ -0.03781, -0.01198, -0.02415, -0.09708, 0.09733,
+ 0.14695, -0.01096, -0.00797, -0.22164, -0.30088,
+ -0.11388, 0.05297, -0.15084, -0.11429, 0.05056,
+ -0.18214, -0.02980, -0.00673, -0.02734, 0.03188,
+ 0.20173, 0.14576, 0.12379, 0.00581, 0.08397,
+ 0.08957, 0.15642, -0.22473, 0.14551, -0.19405,
+ -0.04864, 0.11038, -0.18242, 0.02304, -0.13312,
+ -0.00841, 0.06789, -0.04784, 0.06653, -0.23188,
+ -0.14436, 0.04044, 0.27177, -0.16172, -0.04843,
+ -0.07152, 0.21412, 0.19264, -0.19581, -0.11010,
+ -0.27253, -0.31559, 0.14176, -0.21201, 0.05626,
+ 0.04421, -0.15906, -0.14501, -0.07209, -0.05791,
+ -0.23447, 0.10000, 0.25141, 0.24014, 0.03527,
+ -0.00435, -0.01488, 0.15172, -0.02444, 0.04212,
+ 0.00290, -0.08219, -0.02032, -0.14543, -0.15091,
+ -0.03269, 0.00518, 0.10209, -0.18349, -0.01086,
+ -0.22617, -0.26195, -0.26819, 0.23427, 0.23490,
+ 0.02833, 0.17522, 0.12213, 0.15519, 0.01337,
+ 0.05173, 0.01235, -0.09656, 0.07375, -0.11970,
+ -0.08256, -0.22531, -0.16609, -0.04828, -0.01103,
+ -0.07858, -0.02889, -0.22606, -0.01324, 0.01685,
+ 0.17106, -0.10818, 0.20058, 0.13467, 0.06086,
+ 0.12008, 0.09308, 0.16016, 0.04021, -0.16842,
+ 0.08495, 0.06123, -0.01540, -0.15990, 0.01601,
+ -0.25075, -0.08680, -0.18987, -0.23892, -0.13654,
+ 0.21732, 0.07712, 0.17368, 0.00725, -0.07486,
+ -0.09370, -0.08283, -0.18044, 0.07476, -0.17195,
+ 0.00462, -0.12257, 0.05972, 0.06524, 0.10965,
+ -0.16868, -0.22736, -0.08596, -0.19266, -0.08595,
+ -0.09743, 0.20038, -0.08037, 0.06859, 0.14700,
+ 0.10349, 0.16063, -0.06006, -0.16042, -0.10425,
+ -0.15171, -0.14452, -0.15247, -0.10774, -0.04872,
+ 0.07121, -0.16718, 0.08625, -0.21410, -0.00871,
+ -0.06373, 0.03138, 0.08947, -0.14995, -0.18538,
+ 0.14198, 0.18991, 0.15319, 0.14950, -0.16638,
+ -0.10833, 0.00977, -0.15349, -0.18378, -0.16511,
+ 0.06438, -0.13228, -0.13141, 0.08583, -0.01380,
+ -0.11443, -0.02416, -0.15058, 0.16483, 0.07736,
+ 0.05297, 0.14134, 0.11539, 0.07788, 0.12823,
+ 0.04856, -0.11768, -0.22732, -0.08016, 0.01740,
+ 0.02366, 0.09087, -0.14873, -0.19947, 0.06187,
+ -0.01008, -0.15975, 0.04720, -0.09942, -0.09957,
+ 0.06087, 0.13577, -0.06194, -0.09325, -0.09310,
+ 0.14795, 0.02754, -0.08088, -0.04116, -0.06621,
+ 0.11194, 0.03411, -0.12449, -0.13789, -0.19235,
+ 0.00194, 0.01820, -0.07238, 0.01910, -0.08925,
+ 0.09575, 0.05431, 0.11073, -0.08936, -0.10506,
+ 0.08748, 0.16548, 0.05597, 0.17582, 0.05974,
+ 0.07472, -0.13449, -0.12079, -0.08977, -0.11357,
+ -0.15002, -0.17055, -0.16721, -0.15465, -0.22931,
+ 0.04975, 0.11857, -0.15739, -0.17464, -0.06567,
+ -0.09181, -0.10961, -0.07736, 0.11671, 0.11545,
+ -0.10279, 0.12590, 0.02888, -0.11028, 0.05582,
+ 0.11883, 0.03849, 0.05385, -0.22499, 0.03704,
+ -0.14178, -0.14826, -0.59504, 0.03116, -0.47797,
+ -0.47896, -0.25798, -0.23291, 0.46377, -0.30241,
+ 0.15889, -0.19731, 0.71028, -0.26016, 0.37453,
+ -0.16444, -0.54415, 0.50079, -0.07918, -0.34731,
+ 0.25294, 0.12853, -0.65380, 0.14506, 0.25334,
+ -0.05140, -0.49982, -0.29659, 0.39714, 0.51325,
+ 0.08928, -0.33152, -0.22899, -0.35854, -0.52453,
+ 0.23364, -0.29963, -0.23266, 0.55937, 0.04510,
+ 0.07340, 0.06480, -0.28340, 0.24334, 0.00379,
+ 0.02812, -0.30634, -0.21548, 0.32192, -0.11249,
+ -0.33972, -0.01935, -0.33459, 0.44216, -0.14550,
+ -0.59251, 0.22754, 0.36699, 0.10140, 0.27890,
+ -0.56280, -0.38386, 0.00078, -0.33423, 0.35437,
+ -0.00594, 0.13422, -0.18136, -0.28637, -0.00058,
+ -0.28895, 0.42052, 0.07368, -0.32213, 0.31243,
+ -0.29849, 0.29531, -0.09324, -0.28437, -0.23547,
+ 0.20689, -0.41813, -0.80271, -0.46082, 0.15352,
+ 0.46973, -0.22429, -0.42480, 0.06182, -0.80075,
+ 0.20154, -0.04778, 0.05660, 0.10782, 0.01142,
+ -0.04666, -0.37923, -0.17841, 0.22976, -0.09646,
+ 0.05819, 0.49931, -0.39782, -0.06781, -0.00998,
+ 0.13656, -0.12937, -0.21457, -0.11394, 0.00348,
+ 0.13268, -0.06231, -0.20266, 0.73750, 0.06466,
+ -0.00317, -0.45222, -0.97039, -0.87397, 0.41845,
+ 0.22959, 0.10688, 0.19031, -0.15264, 0.00992,
+ -0.72301, -0.40832, 0.07095, -0.23240, -0.08466,
+ 0.49912, -0.11983, 0.10223, -0.03217, 0.27389,
+ -0.15328, -0.48752, -0.19428, 0.25790, -0.44381,
+ -0.46556, 0.02063, 0.35654, 0.36666, 0.02246,
+ 0.07572, -0.27367, -0.13797, -0.50384, -0.30919,
+ 0.19971, -0.39106, -0.02740, -0.25716, -0.10527,
+ 0.06365, -0.09148, 0.37554, -0.11050, 0.28224,
+ -0.63821, 0.24109, -0.45348, -0.21312, 0.35119,
+ -0.03694, -0.61041, -0.00973, 0.28083, -0.16048,
+ -0.51964, 0.53631, 0.56442, 0.10103, 0.21561,
+ 0.04277, -0.34830, 0.12261, -0.18866, -0.72818,
+ 0.07062, 0.04397, 0.12370, -0.30359, -0.30115,
+ -0.10474, -0.58619, -0.04812, -0.18955, -0.09908,
+ 0.21659, -0.17072, 0.67410, 0.71686, -0.69720,
+ -0.02411, 0.20628, 0.00099, -0.13995, 0.77414,
+ -0.54524, -0.94367, -0.48597, -0.67067, 0.27157,
+ 0.13083, 0.09159, -0.40134, -0.29559, 0.70865,
+ -0.03628, -0.21832, -0.14731, 0.40149, 0.12696,
+ -0.12965, -0.04691, -0.09622, -0.40896, -0.17313,
+ 0.69455, 0.41702, -0.46227, -0.71479, -0.68035,
+ 0.28548, 0.07439, -0.00497, -0.15240, -0.08125,
+ -0.02625, -0.02829, -0.32509, 0.10000, -0.11441,
+ -0.16409, -0.02069, -0.21425, -0.04230, -0.55275,
+ -0.24560, 0.69826, -0.03769, -0.36495, -0.25736,
+ 0.74417, -0.68053, -0.02455, -0.33587, -0.18442,
+ -0.64852, -0.23941, 0.39947, 0.14911, 0.30575,
+ -0.10508, -0.02985, -0.29105, -0.36362, 0.23090,
+ -0.25915, -0.10589, 0.18281, -0.25560, -0.34744,
+ -0.07670, -0.11346, -0.21738, 0.15515, -0.11337,
+ -0.42068, 0.20408, 0.02026, 0.03865, 0.47288,
+ -0.23610, 0.08850, -0.42196, 0.51911, -0.66034,
+ 0.21621, -0.04294, 0.14837, 0.39328, -0.28706,
+ -0.41025, -0.46889, -0.24661, 0.44787, 0.04091,
+ -0.19838, 0.10752, 0.22715, 0.01769, -0.16558,
+ -0.05570, -0.27951, -0.08578, -0.51375, -0.65589,
+ -0.12469, 0.27764, -0.19816, 0.01548, -0.00966,
+ 0.73064, 0.15816, -0.61268, 0.09857, -0.13617,
+ 0.46239, -0.01125, -0.11162, 0.23730, -0.14396,
+ -0.33342, -0.04317, -0.23059, -0.24635, -0.36220,
+ 0.23598, -0.48384, -0.01344, -0.28986, 0.10619,
+ 0.49621, 0.22472, -0.78518, 0.27001, 0.19356,
+ -0.41402, 0.35593, 0.21001, -0.46297, -0.09488,
+ -0.77225, 0.31956, 0.02153, -0.33933, 0.76171,
+ -0.51237, 1.11938, -0.15136, -0.59397, -0.73512,
+ 0.25770, 0.33793, 0.00659, -0.57480, 0.22995,
+ 0.04285, 0.07425, 0.26011, -0.20369, -0.56553,
+ -0.04578, -0.26018, -0.42251, -0.16756, -0.08825,
+ 0.28634, -0.03584, 0.29398, -0.41066, -0.01923,
+ -0.26555, -0.34380, 0.21056, 0.13131, 0.13766,
+ -0.12186, 0.02626, -0.07105, 0.08733, -0.01047,
+ -0.09001, -0.30948, -0.00133, -0.37290, -0.54457,
+ -0.40734, 0.57383, -0.23576, -0.50808, -0.29875,
+ 0.32588, -0.20874, 0.09110, 0.32935, 0.48025,
+ -0.06457, -0.23461, -0.27372, -0.55147, 0.36071,
+ 0.16232, 0.17257, 0.12523, -0.24169, -0.09582,
+ -0.38063, -0.35803, 0.15777, 0.05514, -0.54398,
+ 0.14993, -0.30516, -0.24349, -0.27534, -0.03847,
+ -0.47668, -0.42993, -0.17701, -0.04114, -0.48131,
+ 0.70192, 0.09528, 0.03647, 0.32873, -0.22747,
+ 0.28492, 0.27302, -0.07383, 0.13329, 0.01667,
+ 0.06480, 0.05035, -0.41364, -0.09152, -0.17128,
+ -0.17196, -0.26963, 0.00592, -0.42749, -0.31490,
+ -0.02274, 0.48857, 0.08940, -0.43871, 0.56409,
+ -0.09065, 0.37854, -0.26634, 0.25662, -1.23062,
+ 3.19606, 3.04344, -0.74495, -0.01178, -3.08962,
+ 2.95711, -0.96157, -0.11242, 3.19035, -0.31634,
+ -3.94877, -0.80551, 3.12249, 2.43384, 2.77419,
+ -2.34908, -1.58482, -0.28976, -0.37675, 0.33072,
+ -1.81915, 1.48561, -1.25933, -0.27981, -0.02444,
+ -0.63372, -3.56103, -0.58450, 0.52960, 2.97755,
+ -1.19404, -3.19613, -3.04347, 0.74466, 0.01166,
+ 3.08971, -2.95715, 0.96134, 0.11240, -3.19036,
+ 0.31620, 3.94879, 0.80534, -3.12259, -2.43392,
+ -2.77417, 2.34908, 1.58502, 0.28972, 0.37655,
+ -0.33097, 1.81918, -1.48576, 1.25928, 0.27947,
+ 0.02416, 0.63331, 3.56102, 0.58434, -0.53008,
+ -2.97761, 1.19476
+};
+
+float const m21_2[(na*21+1)*30+(30+1)*2] = {
+ -0.52292, -0.66323, 0.86811, 0.15865, -0.06901,
+ -0.08473, 0.30411, -0.55758, -1.16274, 0.09101,
+ -0.08220, 0.60744, -0.51787, -0.37453, 0.73269,
+ -0.32127, 0.61552, -0.60441, 0.01245, 0.07610,
+ -0.45369, -0.28401, -0.18280, -0.07296, -0.18336,
+ -0.53591, -0.39445, 0.63640, -0.32401, 0.27394,
+ 0.44866, -0.15890, -0.33666, 0.39764, -0.01942,
+ 0.66449, 0.15845, -0.42055, -0.85928, -0.26573,
+ 0.05024, -0.33706, -0.01891, 0.30173, -0.38617,
+ 0.76358, -0.16374, -0.15825, -0.30981, -0.72783,
+ 0.00947, 0.00245, 0.45757, 0.30528, -0.07228,
+ -0.52050, -0.24183, 0.27290, -0.18409, -0.58940,
+ -0.03449, 0.03878, -0.48715, 0.50892, -0.75456,
+ -0.71813, 0.05223, -0.31871, -0.43719, -0.13614,
+ -0.32985, -0.47319, -0.15725, 1.31254, 0.38741,
+ -0.21709, 0.23616, -0.49057, -0.02083, 0.51473,
+ -0.29274, 0.60419, -0.56362, -0.44937, -0.42336,
+ 0.01712, 0.01023, 0.58861, -0.06556, -0.26299,
+ -0.19372, 0.29175, -0.00170, -1.13954, 0.03529,
+ 0.16745, -0.44652, 0.47716, 0.79581, -0.54426,
+ 0.54128, -0.64648, -0.08394, -0.68591, -0.17127,
+ 0.14469, -0.14567, 0.42852, 0.04176, -0.02705,
+ -0.58890, -0.16882, -0.54011, -0.20862, -0.35682,
+ -0.42078, 0.03841, -0.06331, -0.09238, 0.53602,
+ 0.27351, -0.09658, -0.01678, -0.14850, -0.57670,
+ 0.04749, 0.05928, -0.12605, 0.29802, -0.35888,
+ -0.73804, -0.30884, -0.90900, -0.15748, -0.53373,
+ 0.26835, -0.43506, 0.00230, 0.45852, 0.00026,
+ -0.47634, 0.80416, 0.19834, -0.18930, 0.55301,
+ -0.42291, -0.12358, -0.15211, -0.01510, -0.62626,
+ -0.34541, -0.62241, 0.41318, 0.09474, 0.05955,
+ 0.03250, 0.43366, -1.01364, -0.07255, -0.49281,
+ 0.17077, -0.55108, 0.29341, 0.75883, -0.00228,
+ 0.38100, -0.62244, -0.25882, 0.48832, -0.80473,
+ -0.11256, -0.53476, -0.78504, 0.22937, -0.21128,
+ 0.43060, 0.41699, -0.31048, -0.32319, -0.10302,
+ -0.72710, 0.31865, 0.18658, 0.22844, 0.21889,
+ -0.42688, 0.06852, -0.51289, -0.07037, -0.05873,
+ -0.32499, -0.18627, 0.18706, -0.63308, -0.13773,
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+ -0.14674, 0.03203, 0.05205, -0.15800, 0.02043,
+ 0.11524, -0.07650, -0.18510, 0.03076, 0.06151,
+ -0.13944, 0.10278, -0.11400, 0.07919, -0.11960,
+ -0.13601, -0.11400, -0.15247, 0.08849, -0.11382,
+ -0.16942, -0.18193, -0.16390, 0.04954, -0.15914,
+ -0.17570, 0.11387, 0.10392, -0.14855, 0.05271,
+ -0.11132, -0.16000, -0.12499, 0.06749, -0.12896,
+ -0.11161, 0.07422, -0.08791, 0.07538, -0.13364,
+ 0.09055, -0.17908, -0.18652, 0.01650, 0.06770,
+ -0.14879, -0.18233, -0.11400, -0.05619, 0.05421,
+ -0.13893, 0.07817, 0.05974, 0.09441, 0.08539,
+ -0.15487, -0.14004, 0.06619, 0.08340, -0.10738,
+ 0.08410, 0.08887, -0.16474, -0.19275, -0.21104,
+ -0.16532, -0.11874, 0.01461, 0.09563, -0.06612,
+ 0.04290, 0.04488, -0.10569, 0.05445, 0.09172,
+ 0.09617, 0.04353, -0.12272, -0.10919, 0.09413,
+ 0.07172, 0.09219, -0.11556, 0.02619, -0.20937,
+ 0.00981, 0.02683, 0.05037, 0.00710, 0.09950,
+ -0.03532, 0.02796, 0.04857, -0.07080, -0.14368,
+ -0.11481, -0.13566, -0.12800, 0.04446, 0.03258,
+ -0.09250, -0.09602, 0.10656, -0.08349, -0.19915,
+ -0.19119, -0.18176, 0.03550, 0.07055, -0.19667,
+ -0.11374, -0.05862, -0.15796, 0.02701, -0.08143,
+ 0.06969, -0.10164, -0.13679, -0.14669, 0.04827,
+ 0.08303, 0.10738, -0.08767, -0.11784, 0.10000,
+ -0.19747, -0.00305, 0.04522, -0.15849, -0.16364,
+ -0.19342, 0.06898, 0.12720, -0.17149, 0.02488,
+ 0.07972, 0.08775, -0.12667, -0.08712, 0.04216,
+ 0.05211, -0.13224, -0.09538, -0.09087, 0.05829,
+ 0.20382, -0.17022, -0.19513, -0.16242, -0.15502,
+ -0.13764, 0.01866, 0.04326, 0.13443, 0.02097,
+ -0.15402, 0.09145, -0.12550, 0.06746, 0.08962,
+ 0.04800, 0.07811, -0.10905, 0.11823, -0.10805,
+ 0.05764, 0.11950, 0.02290, 0.01477, 0.04311,
+ 0.03856, 0.04423, -0.21803, 0.08451, 0.11909,
+ -0.16803, -0.14043, 0.04941, -0.14614, -0.11500,
+ -0.10722, 0.08915, -0.10502, 0.08709, 0.09844,
+ -0.10733, 0.09348, -0.10741, -0.14246, 0.01784,
+ 0.05769, 0.05010, 0.06824, 0.01592, 0.07920,
+ 0.12733, 0.06969, 0.03324, 0.06314, 0.08132,
+ 0.04884, -0.08456, 0.05201, -0.13201, -0.07803,
+ -0.10593, 0.03725, 0.06816, -0.15692, -0.16806,
+ 0.03669, 0.02964, 0.05799, 0.06199, 0.00207,
+ 0.09867, 0.12827, -0.13209, 0.03491, 0.08207,
+ -0.12339, -0.13238, 0.08617, -0.14265, -0.13886,
+ -0.13081, 0.08845, -0.09106, 0.07727, -0.15480,
+ -0.13865, 0.03717, -0.12565, -0.15071, 0.06344,
+ -0.13767, 0.07234, -0.06889, 0.06666, 0.03060,
+ -0.13634, 0.10795, -0.11907, -0.11934, 0.05743,
+ -0.16371, 0.08313, -0.12014, 0.08440, -0.14569,
+ -0.00715, -0.13622, 0.04133, 0.04459, -0.15470,
+ -0.11837, -0.14682, 0.06322, -0.10119, 0.04335,
+ -0.14291, -0.14520, -0.10585, -0.11327, 0.04760,
+ 0.06022, 0.07327, -0.11422, -0.09357, 0.11277,
+ -0.14139, -0.00255, -0.15368, 0.07117, -0.12775,
+ 0.05370, -0.10318, 0.05006, 0.07524, 0.12225,
+ 0.06376, 0.04865, -0.17046, -0.14153, -0.14783,
+ 0.06535, -0.12887, -0.11580, 0.08292, 0.07261,
+ 0.08378, -0.12431, -0.00598, -0.10887, 0.03590,
+ -0.16076, 0.05865, 0.07337, 0.02829, 0.05826,
+ -0.10065, 0.06111, 0.03089, -0.14348, -0.12918,
+ -0.10509, 0.10158, 0.07853, -0.15222, -0.10003,
+ 0.05641, -0.10718, 0.08267, 0.01179, 0.09120,
+ -0.12831, -0.15751, 0.04507, 0.08248, 0.02978,
+ -0.13106, 0.09055, 0.05259, 0.05434, 0.00897,
+ 0.04591, 0.07162, 0.08804, -0.13639, -0.12545,
+ 0.12037, 0.05730, 0.06743, 0.04955, -0.10649,
+ -0.63610, -0.10626, 0.06662, 0.05080, -0.12187,
+ -0.05864, -0.22209, -0.11545, -0.05386, -0.02610,
+ -0.15197, -0.08945, -0.04653, 0.03210, 0.06312,
+ 0.02768, -0.06204, -0.19115, 0.06488, -0.16649,
+ 0.00725, -0.01959, -0.06555, -0.05228, 0.09966,
+ -0.05988, -0.06288, -0.12688, 0.04141, 0.11044,
+ -0.08225, 0.04898, -0.14893, 0.09235, 0.00713,
+ 0.03065, -0.18314, 0.10491, -0.05688, 0.06079,
+ -0.14278, 0.01883, 0.04706, 0.15049, -0.04220,
+ 0.04755, -0.07501, -0.05542, -0.16603, -0.17202,
+ 0.10021, -0.07382, -0.12034, 0.03925, -0.06664,
+ 0.01507, 0.04026, 0.01660, -0.15530, 0.01317,
+ -0.11569, -0.00217, -0.19033, -0.10685, 0.14764,
+ -0.07647, 0.11211, 0.12092, -0.06497, -0.14344,
+ 0.04253, -0.12611, -0.07159, -0.18802, -0.22501,
+ -0.09417, -0.21359, 0.08859, -0.11725, 0.05217,
+ 0.05346, -0.12941, 0.02943, -0.20936, -0.10648,
+ -0.01086, -0.04278, -0.16958, -0.06422, -0.06556,
+ 0.07716, -0.17065, -0.16601, -0.04985, -0.01243,
+ 0.02732, 0.12160, -0.17341, 0.02006, 0.05861,
+ 0.05296, -0.14620, -0.12799, 0.03356, 0.01258,
+ -0.12302, -0.06630, -0.08883, -0.09185, 0.16786,
+ 0.16769, -0.11829, 0.05148, 0.04383, 0.17321,
+ 0.03883, -0.01407, -0.09171, 0.00048, -0.18046,
+ 0.08256, 0.07459, 0.00982, -0.14802, -0.19022,
+ -0.17533, 0.03600, 0.15280, -0.00275, 0.09735,
+ 0.15532, -0.05956, 0.08567, 0.06960, -0.16569,
+ 0.12801, -0.15530, -0.23394, 0.10592, -0.17229,
+ -0.17675, -0.09320, 0.05154, -0.21359, 0.03426,
+ -0.01118, -0.15707, -0.15803, -0.04356, -0.02495,
+ 0.10501, 0.14058, 0.13012, 0.10936, 0.07594,
+ -0.00505, -0.07387, -0.11855, -0.23988, -0.08834,
+ -0.16347, 0.05246, 0.06846, 0.04816, -0.01861,
+ -0.18245, -0.18329, -0.16379, -0.14306, 0.13007,
+ -0.05703, -0.03949, -0.02437, -0.10209, 0.14168,
+ 0.10027, 0.00446, -0.04941, -0.17760, -0.19544,
+ -0.09435, 0.02512, -0.22566, -0.10135, 0.07616,
+ -0.22801, 0.01921, -0.00834, 0.00656, 0.08107,
+ 0.14294, 0.19164, 0.14233, -0.01109, 0.13569,
+ 0.12448, 0.10273, -0.22823, 0.17118, -0.14173,
+ -0.04314, 0.07767, -0.17144, 0.00295, -0.09452,
+ 0.07013, 0.01130, -0.01263, -0.04575, -0.19841,
+ -0.14536, 0.00423, 0.20828, -0.05844, -0.01365,
+ -0.12163, 0.14799, 0.09282, -0.20291, -0.02211,
+ -0.18673, -0.24315, 0.04736, -0.16552, 0.03134,
+ 0.05099, -0.11925, -0.23691, -0.03439, -0.01723,
+ -0.18059, 0.10000, 0.17938, 0.23555, 0.01886,
+ -0.00478, -0.03152, 0.14994, -0.08663, 0.00122,
+ -0.03449, 0.07888, -0.03637, -0.12565, -0.14747,
+ -0.01271, 0.07767, 0.08110, -0.19328, -0.02537,
+ -0.18408, -0.18917, -0.27054, 0.16868, 0.15058,
+ 0.06394, 0.15595, 0.12729, 0.15061, -0.04270,
+ -0.01910, -0.05018, -0.01602, 0.03736, -0.12614,
+ -0.16077, -0.17571, -0.07084, 0.02272, 0.00382,
+ 0.02468, -0.06853, -0.12494, 0.02983, -0.03870,
+ 0.13028, -0.09932, 0.17374, 0.14104, 0.11724,
+ 0.10340, 0.04365, 0.14672, 0.07046, -0.13948,
+ 0.08678, 0.06694, 0.02739, -0.15498, 0.04479,
+ -0.25337, -0.01087, -0.22441, -0.20438, -0.14597,
+ 0.13793, 0.14381, 0.07074, -0.03603, -0.07812,
+ -0.07654, -0.07596, -0.19414, 0.07341, -0.12674,
+ 0.04691, -0.14207, 0.07718, 0.05098, 0.05163,
+ -0.16791, -0.25447, 0.01873, -0.18182, 0.03361,
+ -0.09009, 0.14523, -0.11188, 0.07773, 0.14239,
+ 0.11777, 0.10098, -0.11251, -0.16938, -0.07913,
+ -0.09843, -0.14894, -0.12517, -0.13368, 0.02662,
+ 0.06636, -0.15665, 0.01375, -0.16695, -0.00422,
+ 0.00578, 0.09139, 0.09351, -0.09814, -0.11673,
+ 0.12104, 0.12628, 0.14193, 0.13760, -0.21414,
+ -0.11261, 0.12657, -0.13797, -0.16712, -0.13720,
+ 0.01661, -0.15057, -0.14958, 0.00907, 0.05504,
+ -0.22759, 0.01728, -0.05224, 0.09027, 0.11350,
+ 0.03798, 0.15158, 0.10773, 0.05902, 0.11379,
+ 0.04116, -0.07731, -0.13657, -0.09039, 0.10598,
+ 0.01199, 0.02901, -0.12259, -0.10780, -0.03246,
+ 0.02372, -0.21954, 0.05546, -0.07350, -0.10493,
+ 0.08559, 0.02084, -0.07070, -0.13071, -0.10854,
+ 0.11395, -0.00981, -0.06006, 0.04263, -0.07074,
+ 0.05829, 0.04000, -0.15305, -0.10188, -0.11788,
+ 0.00263, 0.07627, 0.00649, 0.03893, -0.07627,
+ 0.05708, 0.11108, 0.05967, -0.05629, -0.12696,
+ 0.06966, 0.13794, 0.03642, 0.13860, 0.04198,
+ 0.05989, -0.06270, -0.13775, 0.00032, -0.14240,
+ -0.08932, -0.21812, -0.10776, -0.19064, -0.18214,
+ 0.08270, 0.07962, -0.14260, -0.14776, -0.03885,
+ -0.11611, -0.11233, -0.09464, 0.03537, 0.08014,
+ -0.12026, 0.12794, 0.10419, -0.12158, 0.03838,
+ 0.13048, 0.05654, -0.00565, -0.13298, 0.06363,
+ -0.14501, -0.05731, -0.50832, 0.04033, -0.07086,
+ -0.32566, -0.04091, -0.14936, 0.10138, -0.24486,
+ -0.13515, -0.17763, 0.18075, 0.01453, 0.29791,
+ -0.29431, -0.12635, 0.42497, 0.09042, -0.36643,
+ 0.11239, -0.24628, -0.43521, 0.29136, 0.04485,
+ -0.05338, -0.05222, -0.24516, -0.14079, 0.26618,
+ 0.02849, -0.21604, -0.07905, -0.66578, -0.36001,
+ 0.35402, -0.27558, -0.10333, 0.41436, 0.08999,
+ 0.13959, 0.09636, 0.00176, 0.23232, 0.06507,
+ -0.14402, -0.03342, 0.01939, 0.08192, -0.11136,
+ -0.48340, 0.06930, -0.07187, 0.47797, -0.51074,
+ -0.14099, 0.23513, 0.10847, -0.21820, 0.60251,
+ -0.19879, -0.56824, -0.07773, -0.24263, 0.12299,
+ 0.02772, -0.18526, -0.13664, -0.02698, -0.24601,
+ -0.22296, 0.03980, 0.06222, -0.12995, 0.08494,
+ -0.18056, -0.11090, -0.03465, -0.29627, -0.14006,
+ 0.31595, -0.12241, -0.32979, -0.33168, 0.21213,
+ 0.37442, -0.25150, -0.06289, 0.04282, -0.31574,
+ 0.24274, 0.20748, -0.34993, -0.01200, -0.28263,
+ -0.23417, -0.34564, -0.15067, 0.24707, 0.04488,
+ 0.24929, -0.18070, -0.17303, -0.08243, -0.20803,
+ 0.20519, 0.15560, -0.24947, -0.09068, -0.15311,
+ -0.00198, -0.09163, -0.24142, 0.33205, -0.17834,
+ 0.07734, -0.55855, -0.62925, -0.12242, 0.11567,
+ 0.34497, -0.58436, 0.14378, -0.00052, 0.28904,
+ -0.53382, 0.02216, -0.10615, -0.08509, -0.00632,
+ 0.01783, -0.37348, 0.19536, -0.16217, 0.32233,
+ -0.30671, -0.32175, -0.05386, 0.11798, -0.19348,
+ -0.24316, 0.21138, 0.22123, 0.49264, 0.13423,
+ 0.21679, -0.40099, -0.36544, -0.39127, -0.15878,
+ 0.14764, -0.35108, -0.45840, -0.14272, 0.05936,
+ -0.26010, -0.27714, 0.18775, -0.25629, 0.10177,
+ -0.17122, 0.22060, -0.41405, -0.06949, 0.19103,
+ -0.09112, -0.16160, 0.03288, 0.34624, 0.05813,
+ -0.33998, 0.36664, 0.20234, -0.00034, 0.28442,
+ 0.07479, -0.37878, -0.07270, -0.15202, -0.23492,
+ -0.09961, 0.17253, -0.15783, 0.06315, -0.06693,
+ -0.01277, -0.36045, -0.00734, -0.17009, -0.06948,
+ -0.12255, -0.10288, 0.52064, 0.16756, -0.56184,
+ 0.06084, 0.09274, 0.05956, -0.06295, 0.45672,
+ -0.08618, -0.75562, -0.40064, -0.32443, 0.11409,
+ -0.17429, 0.29149, -0.11201, -0.03020, 0.32640,
+ 0.10995, -0.34398, -0.18739, 0.01566, -0.18897,
+ -0.31365, -0.07084, -0.03755, -0.16422, -0.36229,
+ 0.13373, 0.32320, -0.22933, -0.13718, -0.18705,
+ 0.09566, -0.04329, 0.09631, 0.03908, 0.41210,
+ -0.05591, -0.10763, -0.35350, 0.10000, -0.09509,
+ -0.28380, 0.13906, -0.03787, -0.30020, -0.63500,
+ -0.29306, 0.48187, -0.03790, -0.40788, -0.39340,
+ 0.43283, -0.33718, -0.04562, -0.24071, -0.03022,
+ 0.18755, 0.01434, 0.42548, -0.34723, 0.16838,
+ 0.03324, 0.31473, -0.50361, -0.18821, -0.04172,
+ -0.04760, -0.09892, -0.00601, -0.28193, -0.19050,
+ -0.04561, -0.14075, -0.42582, 0.06342, 0.24947,
+ 0.07513, 0.11992, -0.03076, -0.26737, -0.04796,
+ 0.02520, 0.20639, -0.47146, 0.19466, -0.23428,
+ 0.18513, 0.01312, -0.11631, 0.35888, -0.10054,
+ -0.32728, -0.39417, -0.02536, -0.17442, 0.35999,
+ -0.08824, 0.05006, 0.36217, 0.12091, -0.25793,
+ -0.30471, -0.19255, -0.16676, -0.40457, -0.44582,
+ 0.16826, 0.06961, -0.38941, 0.12313, 0.00699,
+ 0.29420, -0.26330, 0.09409, 0.32273, -0.34345,
+ 0.00273, 0.03804, -0.15703, 0.54420, 0.15198,
+ -0.38334, -0.27803, -0.02030, -0.23500, -0.23635,
+ 0.03366, -0.21482, -0.21559, -0.44099, 0.07260,
+ 0.28547, 0.46672, -0.65411, 0.41618, 0.15884,
+ -0.33006, -0.01935, -0.03752, -0.39712, 0.02489,
+ -0.37853, 0.32298, -0.05537, -0.20258, 0.29499,
+ 0.15896, 0.49052, -0.23038, -0.48342, -0.11376,
+ 0.15019, 0.30674, 0.00300, -0.43440, -0.19568,
+ 0.01022, -0.04837, 0.08781, -0.16940, -0.13684,
+ 0.04406, -0.30703, -0.10107, -0.28498, -0.07722,
+ 0.11283, -0.18637, 0.03851, -0.08489, -0.42013,
+ 0.13569, -0.21246, 0.12050, 0.04086, -0.25592,
+ 0.15344, 0.39005, -0.19789, -0.17306, 0.13298,
+ 0.30904, -0.24169, -0.19909, -0.43988, -0.32764,
+ -0.33096, 0.46301, -0.39548, -0.02966, -0.18486,
+ 0.11427, -0.15878, 0.12318, 0.33290, 0.43395,
+ -0.19368, -0.35080, 0.26961, -0.04952, -0.31704,
+ 0.01314, 0.26169, -0.12472, -0.12254, 0.15614,
+ -0.53424, -0.34265, 0.14732, -0.16781, -0.30365,
+ 0.23135, -0.18737, 0.33309, -0.21557, -0.12718,
+ -0.58371, -0.19621, -0.26000, -0.19321, -0.23063,
+ 0.57534, 0.14280, 0.24740, -0.00072, -0.25305,
+ 0.17413, -0.09245, -0.07614, -0.26198, -0.22969,
+ 0.08803, 0.07587, -0.26474, 0.30510, -0.07720,
+ -0.15354, -0.07911, 0.07913, -0.40112, 0.05628,
+ -0.01959, 0.14404, -0.00471, -0.48230, 0.57463,
+ 0.20362, -0.02022, 0.03386, -0.00263, -1.07342,
+ 3.52297, 3.31019, -0.57969, -0.86260, -3.46494,
+ 3.14679, -0.59153, 0.08097, 0.91925, -0.41916,
+ -3.27021, -0.92422, 2.96632, 2.54720, 2.20213,
+ -1.18915, -2.84927, -0.41173, -0.57426, 0.53642,
+ -3.65248, 2.61981, -0.85349, 1.73219, 0.18844,
+ -1.62876, -3.68587, -0.09151, 0.06895, 2.03958,
+ -1.00062, -3.52300, -3.31020, 0.57956, 0.86249,
+ 3.46486, -3.14679, 0.59126, -0.08103, -0.91936,
+ 0.41905, 3.27016, 0.92408, -2.96633, -2.54722,
+ -2.20221, 1.18923, 2.84929, 0.41166, 0.57425,
+ -0.53663, 3.65245, -2.61990, 0.85359, -1.73222,
+ -0.18860, 1.62867, 3.68585, 0.09111, -0.06913,
+ -2.03965, 1.00107
+};
+
+float const m21_3[(na*21+1)*30+(30+1)*2] = {
+ 0.13428, -0.53482, -0.29001, 0.10455, 0.01339,
+ 0.36688, -0.10255, -0.33326, -0.48110, 0.34561,
+ -0.52848, -0.06863, -0.50466, -0.12641, 0.34839,
+ -0.54371, 0.54851, 0.29983, -0.15600, -0.13141,
+ -0.13929, 0.21303, -0.89481, -0.54559, 0.20239,
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+ -0.45927, 0.64475, -0.61572, -0.13685, -0.51499,
+ 0.05545, 0.22951, 0.13447, 0.57671, 0.22743,
+ 0.14138, -0.60149, 0.07086, -0.89536, 0.31687,
+ -0.19023, 0.68458, 0.04264, -0.20073, 0.37977,
+ -0.77711, -0.72382, 0.09294, -0.29691, -0.61478,
+ -0.01178, 0.11799, 0.23740, -0.33667, 0.08648,
+ -0.39266, -0.29984, -0.29810, 0.41142, -0.30472,
+ 0.52120, -0.68840, 0.30166, 0.20965, -0.71457,
+ 0.29591, 0.41445, -0.28352, -0.27438, -0.34763,
+ 0.17285, -0.29837, -0.66493, 0.01648, 0.14900,
+ 0.27458, -0.46722, 0.31643, -0.42598, -0.00388,
+ -0.41897, 0.97199, -0.63897, -0.26834, 0.54377,
+ 0.00179, 0.30986, -0.02626, 0.12533, -1.61273,
+ 3.41461, 3.32330, -0.13712, -3.06368, -2.17755,
+ 3.52919, -0.59334, -0.10063, 1.48269, -0.46135,
+ -3.23661, -0.63941, 3.19562, 2.86805, 0.10434,
+ -1.39374, -3.31002, -0.13582, 1.24817, -0.41776,
+ -3.51206, 1.90228, -0.17358, 0.28525, 0.91554,
+ -1.25741, -4.06087, -0.59263, 0.75113, 3.48308,
+ -0.85423, -3.41469, -3.32328, 0.13672, 3.06360,
+ 2.17754, -3.52924, 0.59306, 0.10056, -1.48281,
+ 0.46119, 3.23661, 0.63927, -3.19565, -2.86807,
+ -0.10478, 1.39377, 3.31002, 0.13571, -1.24822,
+ 0.41768, 3.51203, -1.90236, 0.17357, -0.28546,
+ -0.91559, 1.25731, 4.06087, 0.59241, -0.75144,
+ -3.48314, 0.85483
+};
+
+float const m21_4[(na*21+1)*30+(30+1)*2] = {
+ 0.26929, -0.90603, -0.12815, 0.19290, 0.07622,
+ 0.12506, 0.43297, 0.05026, -0.25776, -0.37172,
+ 0.41229, -0.39669, -0.31722, 0.03329, 0.29442,
+ 0.31681, -0.30618, -0.16338, -0.67698, 0.01410,
+ -0.33404, 0.57400, 0.06882, 0.01700, -0.11548,
+ -0.80282, -0.10148, 0.10862, -0.19338, 0.68199,
+ -0.05844, 0.01555, 0.11643, 0.44495, 0.14940,
+ -0.00189, -0.22114, -1.45636, -0.90886, 0.09645,
+ 0.36386, -0.21772, -0.18241, 0.75441, -0.48273,
+ 0.67829, 0.20072, -0.70384, 0.31978, 0.11450,
+ -0.80841, -0.18171, 0.12174, -0.10306, -0.18848,
+ -0.56354, -0.69414, 0.69227, -0.26739, -0.75474,
+ 0.07528, 0.87505, -0.34207, 0.00132, -0.00559,
+ 0.25954, -0.37006, -0.63781, -0.64422, -0.20683,
+ 0.66729, -0.44955, -0.44823, 0.70085, 0.11995,
+ 0.49739, 0.77421, -0.09680, -0.22626, 0.22997,
+ -0.40978, -0.34207, -0.25136, -0.60262, 0.31605,
+ 0.86000, -0.29922, -0.32077, -0.07709, -0.72033,
+ -0.17512, 0.35900, -0.01427, -1.10904, -0.78060,
+ -0.08224, 0.34464, 0.36671, 0.33433, 0.12280,
+ -0.08135, -0.01093, -0.03686, -0.38749, -0.04707,
+ 0.27648, 0.12247, 0.06867, -0.14476, -0.24248,
+ -0.78853, 0.13101, 0.79468, 0.18837, -0.03619,
+ -0.59788, -0.45553, -0.20635, -0.46902, 0.03512,
+ 0.74157, -0.85223, -0.38214, 0.61492, -0.54042,
+ 0.10522, -0.19278, -0.02833, 0.43517, -0.36477,
+ -0.18201, -0.26364, 0.19060, 0.07106, -0.91959,
+ -0.05310, -0.81890, -0.60436, 0.05227, 0.21540,
+ -1.27339, 0.23451, 0.54787, 0.04374, 0.87036,
+ 0.17445, 0.02840, -0.32137, -0.14015, -0.85985,
+ -0.07882, -0.06297, 0.21780, -0.37790, 1.12199,
+ -0.36693, 0.33406, -0.36156, -0.27815, -0.36394,
+ -0.10275, -0.47935, -0.35280, 0.43004, 0.25652,
+ 0.50045, -0.42564, -0.12189, 0.51870, -0.58144,
+ 0.46166, -0.64809, -0.49552, -0.51222, -0.21186,
+ 1.10946, 0.05757, 0.00651, -0.04131, -0.19036,
+ -0.46824, -0.29291, -0.13895, 0.00423, 0.07292,
+ -0.48787, -0.13468, -0.10934, 0.04853, -0.46747,
+ -0.16949, 0.09007, -0.19705, -0.62543, -0.80562,
+ -0.23471, 0.16965, 0.35625, 0.54871, 0.46882,
+ -0.34933, -0.29267, -0.30589, -0.42507, 0.16656,
+ -0.15285, -0.08635, 0.10757, 0.26238, -0.09132,
+ -1.13690, -0.55095, 0.36415, 0.12218, -0.01017,
+ -0.26745, -0.55804, 0.20162, 0.43083, 0.20912,
+ -0.01990, 0.28578, 0.37615, 0.04354, -0.72477,
+ -0.32738, -0.19126, -0.00420, -0.08365, 0.50791,
+ 0.10000, -0.43983, -1.10445, 0.23635, -0.61906,
+ 0.25968, -0.10549, 0.24040, 0.13073, 0.00625,
+ -0.22821, 0.11695, -0.26701, 0.59966, -0.19738,
+ 0.33082, -0.17292, 0.28861, -0.19893, -0.44389,
+ -0.04809, 0.38247, -0.35755, -1.39092, -0.68835,
+ 0.11069, 0.02931, -0.99945, 0.18165, 0.20487,
+ -0.46889, -0.24376, 0.70370, 0.36478, 0.33544,
+ 0.54809, 0.97624, -0.11361, -0.47156, 0.51597,
+ -0.32592, -0.18984, -0.15514, -0.61555, 0.22860,
+ 0.13548, 0.11458, -0.17536, -0.47676, -0.68112,
+ -0.32363, -0.44784, 0.30225, 0.16568, -0.72214,
+ -0.21906, 1.01805, 0.28447, 1.11264, -0.53823,
+ -0.94006, 0.68681, 0.00906, -0.15214, -0.24167,
+ -0.63291, 0.24327, -0.01230, -0.46045, 0.11791,
+ -0.38014, 0.09300, -0.27938, -0.37293, 0.24870,
+ 0.15345, 0.63523, 0.17705, -0.00763, -0.06038,
+ -0.40518, 0.26330, -0.18355, -0.41526, -0.11436,
+ -0.33026, 0.48644, 0.32070, -0.15513, -0.52537,
+ -0.12704, 0.02282, -0.39842, 0.16927, 0.65782,
+ -0.40326, 0.49891, 0.01507, -0.23391, -0.62808,
+ -0.89852, -0.44439, 0.58470, -0.10241, 0.26866,
+ -0.21178, 0.28707, -0.36031, -0.21581, 0.00598,
+ 0.48820, 0.21194, 0.74402, 0.80163, -0.50163,
+ 0.33546, -0.24809, -0.14788, -0.59912, -0.45305,
+ 0.62806, 0.59594, -1.15800, -0.90641, -0.96819,
+ 0.77850, -0.55251, 0.06902, 0.88921, -0.80908,
+ 0.01436, -0.31095, -0.36462, 0.42010, 0.19947,
+ -0.87968, 0.61918, -0.49761, -0.28843, -0.21414,
+ -0.09029, 0.03259, 0.74906, -0.50935, 0.37679,
+ -0.51277, 0.24298, -0.37126, -0.42965, -0.00612,
+ -0.67304, 0.02648, -0.31877, 0.76736, -0.18448,
+ 0.72847, -0.18561, 0.54435, -0.30249, -0.49332,
+ 0.60384, 0.21354, -0.30683, -0.56794, -0.24376,
+ 0.44615, -0.05549, -0.14450, -0.45431, -0.63133,
+ -0.39832, -1.09106, -0.32210, 0.21477, 0.39886,
+ -0.03527, 0.33554, 0.52513, 0.28355, 0.22312,
+ -0.00758, -0.42317, -0.34163, 0.81390, -0.41225,
+ -0.04245, -0.00939, -0.31914, 0.35512, -0.55334,
+ -0.04337, -0.14598, -0.44789, 0.91307, -0.03128,
+ -0.08423, -0.01977, -0.40471, -0.22246, -0.00420,
+ -0.09697, -0.01957, -0.57094, 0.08189, 0.38484,
+ -0.74537, -0.48645, -0.25049, -0.42666, 0.82420,
+ -0.24097, -1.46584, -0.20632, 0.12398, -0.18249,
+ 0.08898, 0.11059, 0.03487, 0.14176, 0.03751,
+ 0.09646, 0.03150, 0.08718, -0.01505, 0.05764,
+ -0.12402, -0.26159, 0.04347, 0.05057, 0.07355,
+ 0.03180, 0.10614, 0.12835, -0.15367, -0.11113,
+ -0.04897, 0.07031, -0.17394, -0.15695, 0.12484,
+ 0.02298, -0.16934, -0.06626, -0.06406, -0.09064,
+ -0.16062, 0.16383, 0.02576, -0.25642, -0.09354,
+ -0.10772, 0.05238, -0.00422, -0.14776, -0.05064,
+ -0.10900, -0.07861, 0.07980, 0.06985, 0.06433,
+ -0.07155, 0.01747, -0.33297, -0.24449, 0.07525,
+ -0.08365, -0.17070, -0.22841, 0.05755, 0.16729,
+ 0.14960, 0.04691, 0.11485, 0.17822, 0.00375,
+ -0.12428, 0.02704, 0.01824, 0.07285, -0.01630,
+ -0.03272, -0.10773, -0.08933, -0.01944, 0.22037,
+ -0.14679, -0.25812, -0.02725, 0.02503, -0.07163,
+ -0.17690, 0.02513, -0.18169, 0.03326, -0.15204,
+ 0.03703, 0.00167, 0.16897, -0.22014, -0.14922,
+ -0.15163, -0.19474, 0.13008, 0.07306, 0.17175,
+ -0.02474, 0.08173, -0.15066, 0.14497, -0.01575,
+ 0.04498, -0.04617, -0.22111, -0.19031, -0.09481,
+ 0.03056, 0.06709, -0.06279, -0.03016, -0.21143,
+ 0.03542, 0.01309, -0.26683, -0.12232, 0.10007,
+ -0.17177, 0.23468, 0.19600, -0.06375, 0.15180,
+ -0.13033, 0.03692, 0.12006, -0.18173, 0.03159,
+ 0.23381, -0.17605, -0.08006, -0.28933, -0.07516,
+ 0.14775, 0.02567, 0.02475, 0.05218, -0.06651,
+ -0.06669, 0.06550, 0.07874, -0.18215, -0.06768,
+ 0.12516, 0.16313, -0.11212, -0.21832, -0.22259,
+ -0.06042, 0.08711, 0.12286, 0.12432, -0.33847,
+ -0.14805, 0.03401, -0.18629, -0.10747, 0.01069,
+ 0.02389, 0.21421, -0.21144, 0.09188, -0.03998,
+ -0.21754, 0.10365, -0.06470, 0.12393, 0.21590,
+ 0.02841, 0.10539, 0.17869, 0.12820, 0.11226,
+ -0.27234, -0.38696, -0.05806, -0.00887, -0.19772,
+ -0.22264, -0.16228, 0.06975, -0.28642, -0.05091,
+ 0.13117, 0.03430, 0.21375, 0.01874, -0.02741,
+ 0.10303, 0.13904, -0.08270, 0.05472, 0.16315,
+ 0.08584, -0.14952, -0.07582, -0.10964, -0.01265,
+ 0.05902, -0.19749, 0.07849, -0.07382, -0.03791,
+ -0.10156, -0.04551, 0.15591, -0.31536, 0.22333,
+ -0.16904, -0.08432, 0.15170, 0.08422, -0.06799,
+ 0.18451, 0.16064, -0.28454, -0.36585, -0.03488,
+ -0.03718, 0.24578, -0.03928, -0.14763, -0.04925,
+ -0.20732, -0.12082, 0.22010, -0.14676, 0.01672,
+ -0.02571, -0.15662, -0.17463, -0.20395, -0.13705,
+ -0.15545, 0.16144, -0.10000, -0.11502, -0.26845,
+ -0.01507, -0.01549, -0.19590, -0.40477, 0.06984,
+ 0.17912, -0.26098, -0.18370, -0.07962, -0.12707,
+ 0.10266, 0.08478, 0.08413, 0.03427, -0.10836,
+ 0.19610, -0.14468, 0.04809, 0.37725, -0.25891,
+ -0.25104, -0.15222, 0.05351, -0.13224, -0.39683,
+ 0.04416, -0.05553, -0.07409, -0.03317, -0.01466,
+ -0.07844, 0.21585, 0.15885, -0.00302, -0.11073,
+ -0.35084, 0.02601, 0.01265, -0.12228, -0.01994,
+ -0.18563, 0.05489, 0.07848, 0.03536, -0.17593,
+ -0.33326, -0.15446, 0.12224, -0.18713, -0.08762,
+ 0.01518, -0.26349, -0.17752, -0.03790, 0.04843,
+ -0.21261, -0.14376, -0.09191, 0.08133, -0.03992,
+ -0.08768, -0.10131, -0.28417, -0.22722, -0.17523,
+ 0.00730, 0.05626, -0.10074, -0.07060, -0.14827,
+ -0.15751, -0.08176, 0.13849, -0.17147, -0.06767,
+ 0.05628, -0.07828, -0.17416, -0.11966, 0.00013,
+ -0.12386, 0.08056, 0.04004, 0.02494, -0.22341,
+ -0.16569, 0.02693, -0.21996, -0.05225, 0.10824,
+ -0.02187, -0.24339, -0.07183, -0.04103, 0.05672,
+ -0.05468, -0.16454, 0.13253, -0.24599, -0.10013,
+ 0.00927, -0.18350, -0.15331, 0.12680, 0.04525,
+ -0.23266, 0.09069, -0.23485, -0.21078, -0.13907,
+ -0.09826, -0.24325, 0.09343, 0.19525, -0.05350,
+ 0.09909, -0.15687, 0.07723, 0.10585, -0.35763,
+ 0.15427, -0.08836, -0.11327, -0.00225, 0.12616,
+ 0.11374, -0.20388, -0.22868, 0.03808, 0.02099,
+ 0.09605, 0.14580, -0.07296, -0.08952, -0.09399,
+ 0.06576, -0.04441, 0.08151, 0.07901, -0.02140,
+ -0.05060, 0.17453, -0.17554, 0.07425, -0.17873,
+ -0.10428, -0.06884, -0.01114, 0.10000, -0.21359,
+ -0.16406, 0.07874, 0.15329, -0.00076, 0.10363,
+ -0.06796, -0.18295, 0.15553, -0.17246, 0.00497,
+ -0.12285, -0.04043, 0.21633, -0.13259, -0.06608,
+ -0.00867, -0.10061, 0.11995, -0.20559, -0.16271,
+ -0.18373, 0.02475, -0.15929, 0.09580, -0.02007,
+ -0.10888, -0.06832, -0.03183, 0.15880, 0.09344,
+ -0.16348, -0.14794, -0.19836, 0.04467, -0.08839,
+ -0.07213, 0.02932, -0.08204, 0.19673, 0.04409,
+ -0.00692, 0.07489, -0.01335, 0.03624, -0.06016,
+ -0.07938, -0.12120, -0.34968, 0.08469, 0.01064,
+ 0.13444, -0.25804, -0.23482, 0.07739, 0.05179,
+ -0.10833, -0.12157, -0.02004, -0.75287, 0.09691,
+ 0.08799, -0.12353, -0.11642, 0.09663, -0.11404,
+ 0.10868, -0.11758, 0.10890, 0.05856, -0.12441,
+ -0.11413, -0.13379, -0.13381, -0.14374, -0.15043,
+ -0.14666, -0.10272, -0.18814, 0.04679, -0.01506,
+ 0.06920, -0.12459, -0.15404, 0.08469, -0.09648,
+ -0.13221, -0.10465, 0.10208, 0.07982, 0.08768,
+ -0.12265, 0.07699, -0.11990, -0.14198, 0.09445,
+ 0.06074, 0.06346, -0.12539, -0.16854, 0.06173,
+ -0.01039, 0.05367, 0.08036, -0.12759, 0.07107,
+ 0.10624, 0.07269, -0.11687, -0.13111, 0.09316,
+ 0.06889, 0.05162, -0.11487, 0.08095, 0.06252,
+ -0.13096, -0.13624, -0.11606, -0.11240, 0.04206,
+ 0.07011, 0.01277, 0.08311, 0.07989, -0.16670,
+ 0.09541, -0.12668, 0.06701, 0.08995, -0.12751,
+ -0.11427, -0.12880, 0.04795, -0.10601, 0.10297,
+ 0.05669, -0.11501, -0.12325, -0.15971, 0.08708,
+ 0.02733, -0.11122, -0.17822, -0.12477, 0.09337,
+ -0.15393, 0.08831, 0.10865, 0.07919, 0.09865,
+ -0.12209, 0.11418, 0.05116, 0.08187, -0.10935,
+ 0.04187, 0.03457, -0.11451, 0.06194, -0.15523,
+ -0.13631, -0.17726, -0.12197, 0.04155, -0.13005,
+ 0.06704, -0.11773, 0.07721, -0.10691, -0.18086,
+ 0.11513, 0.05019, 0.09102, 0.09672, -0.13052,
+ 0.06137, 0.06069, -0.11003, -0.14023, 0.09584,
+ -0.17849, -0.11624, 0.05616, -0.12746, -0.15261,
+ 0.08899, -0.11257, -0.15320, -0.11680, 0.08329,
+ 0.10873, -0.09587, -0.13380, 0.07953, -0.18982,
+ 0.05301, -0.11780, -0.11451, -0.14629, 0.06266,
+ 0.09330, -0.17447, 0.13152, 0.01588, -0.13772,
+ 0.05616, 0.09592, -0.12296, -0.13855, 0.07229,
+ -0.09570, 0.09477, 0.07728, -0.13687, 0.10251,
+ 0.06234, -0.14881, -0.13736, -0.11725, -0.15841,
+ -0.12857, 0.07269, 0.04707, 0.06472, -0.13311,
+ 0.04393, -0.13574, 0.09465, 0.06900, -0.14320,
+ 0.08289, -0.09651, -0.14520, -0.11133, 0.06116,
+ -0.10053, 0.05403, -0.12910, -0.08486, -0.14028,
+ 0.06957, 0.04163, -0.16421, 0.05433, 0.05155,
+ -0.14222, -0.12429, -0.11690, -0.11625, 0.11038,
+ 0.07345, -0.10827, 0.11517, -0.16221, 0.07711,
+ -0.11481, 0.07640, -0.17415, 0.04916, -0.08936,
+ -0.15522, -0.16615, 0.02870, -0.12478, -0.12688,
+ 0.06057, 0.04213, -0.11023, -0.10457, 0.11377,
+ -0.09812, 0.04920, 0.09167, -0.08569, 0.06749,
+ 0.08830, -0.12840, -0.12605, 0.01835, -0.15567,
+ -0.11963, 0.07578, 0.06284, -0.15487, 0.07405,
+ 0.05398, -0.12836, -0.16196, 0.04352, 0.10000,
+ -0.10450, -0.09128, -0.15102, 0.09030, -0.10278,
+ 0.04690, 0.08406, -0.10890, -0.10342, 0.02903,
+ -0.14433, 0.09424, -0.13387, -0.16371, 0.05774,
+ -0.15018, 0.06681, 0.10572, -0.17118, -0.17269,
+ 0.10328, 0.07327, -0.11487, 0.03647, 0.09055,
+ -0.09730, -0.15492, 0.10317, 0.09402, -0.08990,
+ 0.04463, 0.06635, 0.08011, -0.12578, -0.13049,
+ -0.15562, 0.07802, 0.04839, -0.10471, -0.16534,
+ -0.16656, -0.12933, -0.10244, 0.09651, 0.05933,
+ 0.11065, 0.10220, -0.15590, -0.09160, 0.09216,
+ 0.08259, -0.17874, 0.02545, -0.10453, 0.10062,
+ 0.04782, 0.04811, 0.06155, -0.12772, -0.12024,
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+ -0.17427, 0.19751, 0.29296, -0.09766, 0.19972,
+ 0.08184, -0.16998, -0.36697, 0.10000, 0.11321,
+ -0.41658, -0.27745, 0.13340, -0.32316, -0.23748,
+ -0.50437, 0.83652, 0.02607, -0.77193, -0.67567,
+ 0.69409, -0.51898, 0.53773, -0.71373, -0.47215,
+ 0.05253, -0.13818, 0.52124, -0.31551, 0.37056,
+ 0.38350, -0.08684, -0.46901, -0.10468, -0.26612,
+ -0.06222, -0.29605, -0.08117, -0.40503, -0.58446,
+ 0.14899, 0.10323, -0.77715, 0.33132, -0.21565,
+ -0.12426, 0.27715, 0.29801, 0.20247, -0.25470,
+ 0.10200, 0.15080, -0.56906, -0.30384, -0.43026,
+ -0.43837, 0.21451, -0.18376, 0.52341, 0.45967,
+ -0.61264, -0.34736, -0.19869, 0.15459, 0.51985,
+ 0.28488, -0.09313, 0.27460, -0.28046, -0.00007,
+ -0.34372, -0.06162, -0.45633, -0.48633, -0.50325,
+ 0.40918, -0.06330, -0.20105, -0.12126, 0.16300,
+ 0.51467, -0.26030, -0.17001, 0.45023, -0.58223,
+ 0.14599, 0.16721, -0.38758, 0.08218, 0.31609,
+ -0.08696, -0.52896, 0.11841, -0.07772, -0.63757,
+ 0.50316, -0.17174, -0.64199, -0.10418, 0.00053,
+ 0.36882, 0.34370, -0.65017, 0.43990, 0.28939,
+ -0.19478, 0.02126, -0.23075, -0.74912, -0.56853,
+ -0.36929, 0.50076, 0.09774, -0.24989, 0.42342,
+ 0.18342, 0.43485, -0.04883, -0.73117, -0.63733,
+ 0.31055, 0.36355, 0.06391, -0.55285, 0.22869,
+ -0.08953, -0.59816, -0.16099, -0.10825, 0.03857,
+ 0.40588, -0.08630, 0.05735, -0.81126, -0.16599,
+ 0.12790, -0.24845, 0.10626, -0.23803, -0.26331,
+ 0.33906, -0.25451, 0.05775, 0.10964, -0.09871,
+ -0.06113, 0.32793, -0.46711, 0.06467, 0.51115,
+ -0.27496, -0.24913, -0.38079, -0.13321, -0.44603,
+ -0.61018, 0.38463, -0.54705, 0.25709, -0.33872,
+ 0.04454, -0.13017, 0.06025, 0.52972, 0.34811,
+ -0.04952, -0.26949, -0.17838, -0.65923, 0.15172,
+ -0.09931, 0.37294, -0.09031, -0.07229, 0.28023,
+ -0.44623, -0.63004, -0.25988, -0.43818, -0.19998,
+ 0.32506, 0.00105, 0.09586, -0.27743, 0.01036,
+ -0.73790, -0.22339, -0.26809, 0.12705, -0.46749,
+ 0.93078, -0.14600, 0.30192, 0.17683, -0.34094,
+ 0.50379, -0.14649, -0.44889, -0.21773, -0.19978,
+ 0.29368, 0.10864, -0.36827, 0.45752, -0.21044,
+ 0.01307, -0.34993, 0.02468, -0.67006, 0.25826,
+ 0.11214, 0.34028, 0.02159, -0.10376, 0.38316,
+ -0.05185, 0.25178, -0.54169, -0.43340, -1.50171,
+ 3.28135, 0.46062, 0.25110, -2.23754, -3.41884,
+ 3.01752, -1.49866, 0.22576, 0.02939, -0.39703,
+ -3.37802, -0.79799, 3.00261, 2.72336, 3.19433,
+ -0.37721, -2.64971, -0.21804, 0.56392, -0.11288,
+ -3.79731, 2.73510, -0.19209, -0.08090, -0.21032,
+ -1.29121, -4.10561, -0.63698, 0.24017, 3.12024,
+ -0.49117, -3.28132, -0.46082, -0.25157, 2.23748,
+ 3.41883, -3.01757, 1.49862, -0.22578, -0.02966,
+ 0.39689, 3.37803, 0.79783, -3.00261, -2.72341,
+ -3.19433, 0.37716, 2.64977, 0.21798, -0.56415,
+ 0.11280, 3.79727, -2.73513, 0.19223, 0.08075,
+ 0.21035, 1.29114, 4.10562, 0.63669, -0.24037,
+ -3.12025, 0.49168
+};
+
+float const m21_5[(na*21+1)*30+(30+1)*2] = {
+ -0.43101, -1.19925, 0.64860, 0.14419, -0.02141,
+ -0.47490, 0.24581, -0.48752, -0.43563, 0.09569,
+ -0.12159, 0.24270, 0.26140, 0.14787, 0.42933,
+ -0.31381, 0.47705, -0.23501, -0.05057, -0.14967,
+ -0.26599, -0.16163, -0.70878, -0.27445, -0.14824,
+ -0.08976, 0.01197, 0.03800, -0.16754, 0.64086,
+ 0.11253, 0.10707, -0.05412, 0.35439, -0.42520,
+ 0.71554, -0.43358, -0.27026, -0.45415, -0.05955,
+ -0.01680, -0.00402, -0.21493, -0.10242, -0.35478,
+ 0.47202, 0.22831, 0.17932, -0.23084, -0.51507,
+ 0.01661, -0.05220, 0.34749, 0.21493, -0.50106,
+ -0.25970, -0.33501, 0.23851, 0.29982, -0.35674,
+ -0.10829, -0.04404, -0.20521, -0.03263, -0.55894,
+ -0.01764, 0.14855, -0.01770, 0.00953, 0.12995,
+ -0.09954, -0.30599, -0.54972, 1.00144, 0.31082,
+ -0.22803, 0.15099, 0.14089, -0.49380, 0.22316,
+ -0.21746, -0.22786, -0.33171, -0.31757, -0.51943,
+ 0.39826, 0.06285, -0.15575, -0.00787, -0.31997,
+ 0.05078, 0.10929, 0.07352, -0.70531, 0.42657,
+ 0.22500, -0.28505, 0.00010, 1.04243, -0.27559,
+ -0.01599, -0.23313, -0.40846, -0.76372, 0.01822,
+ -0.03336, -0.07926, 0.48251, 0.22678, -0.02286,
+ -0.23720, 0.07575, -0.51475, 0.10365, -0.51653,
+ 0.08480, 0.12715, 0.38184, -0.08927, -0.25257,
+ 0.32688, -0.31120, -0.36456, -0.46642, -0.41293,
+ 0.01378, -0.40023, 0.20505, 0.10923, -0.00571,
+ -0.06926, -0.33148, 0.11225, 0.01291, -0.40189,
+ 0.18298, -0.53270, -0.29059, 0.30487, 0.05106,
+ -0.49901, 0.62911, 0.05326, -0.61523, -0.02777,
+ 0.11138, -0.27000, 0.04715, 0.21315, -0.19224,
+ -0.05661, -0.34776, 0.65912, -0.35725, 0.29595,
+ -0.16546, 0.33317, -0.59411, -0.02237, -0.64184,
+ -0.31534, -0.60026, 0.49485, 0.16269, -0.25874,
+ 0.42938, -0.54874, -0.20457, 0.48868, -0.00296,
+ -0.10031, -0.43264, 0.03586, -0.00922, -0.21521,
+ 0.24489, 0.04367, -0.30993, -0.23221, 0.22933,
+ -0.91000, -0.32053, -0.37161, 0.16436, 0.32560,
+ -0.47853, 0.19873, -0.07098, -0.14705, -0.11389,
+ -0.45390, -0.18366, 0.06831, -0.46000, 0.20791,
+ 0.01153, -0.14732, -0.00997, -0.07486, -0.61735,
+ -0.12746, -0.16939, 0.02914, -0.61135, 0.15005,
+ 0.43855, 0.25363, -0.31084, 0.45668, -0.20587,
+ 0.24973, -0.07680, -0.98364, -0.15674, -0.16526,
+ -0.14001, -0.36031, -0.10403, 0.29828, -0.30653,
+ -0.27860, 0.35965, 0.13850, -0.37680, -0.35689,
+ 0.35007, 0.02178, 0.13025, 0.18565, 0.40777,
+ 0.10000, 0.12529, -0.04665, -0.58999, -0.19752,
+ -0.62899, 0.31696, -0.36549, 0.44378, 0.88382,
+ -0.34762, -0.48060, -0.13332, 0.68328, -0.08038,
+ -0.35667, 0.19884, 0.15518, -0.42430, -0.33186,
+ -0.14735, 0.25955, -0.41275, -0.25923, -0.04082,
+ 0.01081, -0.21205, -0.21804, 0.31602, 0.20362,
+ 0.10452, -0.46310, -0.22518, -0.52960, -0.32175,
+ 0.17947, 0.92079, -0.08666, -0.01387, -0.11965,
+ 0.12728, -0.06052, -0.16436, -0.32911, -0.13437,
+ 0.40062, 0.26344, 0.10158, -0.71737, -0.34384,
+ -0.06352, -0.20037, -0.11122, -0.16970, -0.70371,
+ 0.44540, 0.61372, 0.68171, 0.20397, -0.10094,
+ -0.69524, 0.40563, -0.51631, -0.09613, -0.31757,
+ -0.03244, 0.47224, -0.19543, -0.43596, -0.82514,
+ -0.06703, -0.18072, 0.46981, -0.14735, -0.37165,
+ -0.45206, 0.24970, 0.55872, -0.15702, 0.02660,
+ 0.14259, -0.13924, 0.01276, -0.34878, 0.27219,
+ -0.54972, 0.26579, 0.51392, -0.24651, -0.49786,
+ 0.05776, 0.04411, 0.49295, 0.15257, -0.07823,
+ 0.10070, 0.07927, -0.38121, 0.15630, 0.00524,
+ -0.20663, -0.04416, -0.15158, -0.19005, -0.81508,
+ 0.02661, -0.11733, -0.23601, 1.00620, -0.28021,
+ 0.15491, -0.46862, 0.28689, 0.50522, 0.55653,
+ -0.64436, 0.27227, -0.17718, -0.59221, -0.56873,
+ -0.24405, 0.49134, -0.32052, -0.25407, -0.31443,
+ 0.10037, -0.22185, 0.00208, 0.29951, -0.19414,
+ -0.22802, -0.21312, -0.41007, -0.09774, 0.28777,
+ -0.07815, 0.40518, 0.10458, -0.39186, -0.14402,
+ -0.02853, 0.20055, 0.17833, -0.16650, -0.14932,
+ 0.23356, -0.45771, -0.21847, -0.24421, 0.28558,
+ -0.11337, -0.04833, -0.80422, 0.07202, -0.30912,
+ 0.56584, -0.25274, -0.15783, 0.06110, 0.04930,
+ -0.21493, 0.12470, -0.41136, 0.29320, -0.08110,
+ 0.41418, 0.14682, 0.08419, -0.32580, 0.17418,
+ -0.26603, -0.42188, -0.19740, -0.64838, -0.27636,
+ -0.08568, 0.47204, 0.14506, 0.07315, -0.04919,
+ -0.15455, -0.08905, -0.12663, -0.10744, 0.15603,
+ 0.17060, 0.08820, -0.12621, 0.54755, -0.54417,
+ 0.31201, -0.51326, -0.35271, 0.31801, 0.25193,
+ -0.00482, -0.12120, 0.30898, -0.02519, -0.23670,
+ -0.70379, 0.13636, -0.23475, -0.15035, -0.29301,
+ 0.04229, -0.56482, -0.23989, 0.28128, 0.40253,
+ -0.47936, -1.32538, -0.50639, -0.01373, -0.59487,
+ 0.44953, 0.89612, 0.41904, 0.17379, -0.09980,
+ 0.47265, -0.73534, -0.03480, -0.51521, -0.14806,
+ -0.54984, -0.74828, 0.19484, -0.45584, 0.69003,
+ -0.01514, 0.65946, 0.10672, -0.40925, 0.48783,
+ -0.02323, -0.23182, 0.11152, 0.11220, 0.42688,
+ -0.04493, -0.63039, 0.07795, -0.45121, 0.08023,
+ -0.28643, 0.19599, -0.67519, -0.69073, -0.54438,
+ 0.13938, 0.07538, 0.48109, -0.34755, -0.45150,
+ 0.24965, -0.34533, -0.03505, 0.34162, -1.37912,
+ 0.38628, -0.07185, -1.10499, 0.22400, 0.60469,
+ 0.48852, -0.10001, -0.38231, 0.06388, 0.64858,
+ -0.51087, -0.07948, 0.22232, 0.07221, 0.01755,
+ -0.31581, 0.08469, 0.23807, -0.38598, 0.15535,
+ -0.44330, -0.31138, 0.01012, -0.60224, 0.11518,
+ 0.55073, -0.62473, 0.67163, -0.16090, -0.54323,
+ -0.20020, 0.45361, 0.64868, -0.15813, -0.71313,
+ -0.21023, -0.01124, 0.36714, -0.58928, -0.51867,
+ 0.23022, -1.16087, 0.08156, 0.52427, 0.57560,
+ -0.01877, -0.14754, -0.70801, 0.40566, 0.04574,
+ -0.43922, -0.06100, -0.34108, -0.04119, 0.50849,
+ -0.15577, 0.11274, -0.12791, -0.39366, -1.06844,
+ 0.28794, 0.00618, -0.49108, -0.01750, 1.55897,
+ -0.30921, 0.85969, -0.62415, 0.13123, -0.29748,
+ -0.43145, 0.13603, 0.11797, -0.47555, 0.20318,
+ 0.20287, -0.18827, -0.21242, -0.35882, 0.39345,
+ 0.65084, 0.23724, 0.25000, -0.42728, -0.06573,
+ 0.23403, -0.19982, 0.42633, -0.99500, -0.01018,
+ 0.50362, -0.29987, -1.03660, -0.27843, -0.39000,
+ -0.16981, 0.21988, 0.08455, 0.10691, -0.53407,
+ 0.21977, 0.32129, 0.02132, -0.16781, -0.04032,
+ -0.14985, 0.32474, -0.21435, -0.06364, -0.63850,
+ -0.51671, -0.02557, -0.15867, 0.24130, 0.07169,
+ 0.05054, 0.41280, -0.45762, 0.94563, -0.36422,
+ -0.37830, -0.57607, -0.74497, 0.16665, -0.75301,
+ -0.78641, -0.03410, 0.59460, 0.31320, 0.26288,
+ 0.48181, -0.15651, 0.35753, -0.03877, 0.44529,
+ -0.09812, 0.02796, -0.00622, -0.85890, 0.29326,
+ -0.03446, -0.20141, -0.52816, 0.24698, -0.33141,
+ 0.01100, -1.12211, -0.00108, 0.09264, 0.78058,
+ 0.06167, -0.40318, 0.05246, -0.07313, 0.12868,
+ -0.44806, 0.49198, -0.55483, 0.02148, 0.40902,
+ 0.24782, -0.00363, -1.13891, -1.06797, 0.72141,
+ 0.61711, -0.10981, -0.04460, -0.40615, 0.21428,
+ 0.29026, 0.44273, -0.10828, -0.34827, 0.53118,
+ -0.15238, -0.42064, -0.53633, -1.19717, 0.54974,
+ -0.65476, 0.40880, -0.10000, -1.09961, -0.77287,
+ 0.28988, -0.10974, -0.04224, -0.41629, 0.12484,
+ 0.17743, -0.86552, 0.45731, -0.66135, -0.05943,
+ 0.04020, -0.06208, 1.29789, -0.19352, -0.22346,
+ -0.08815, -0.31251, 0.61161, 0.39777, -0.21824,
+ 0.16017, -0.24211, 0.52534, -0.32123, -0.97902,
+ -0.15399, -0.23229, -0.79610, 0.28212, -0.02150,
+ 0.32859, 0.22498, -0.10200, 0.63525, -0.23490,
+ -0.72237, 0.01977, -0.33642, -0.04925, -0.07771,
+ 0.15324, 0.21497, 0.01050, 0.27814, 0.13700,
+ -0.19009, -0.51378, -0.67149, -0.89638, -0.23777,
+ 0.14672, -0.05205, -0.61982, 0.23326, -0.22960,
+ -0.45891, -0.53103, 0.18733, 0.30929, 0.49087,
+ -0.27221, -0.20825, -0.08129, -0.42144, -0.46912,
+ -0.25338, -0.10167, 0.13924, -0.00483, -0.04367,
+ -0.04838, 0.40191, -0.26313, 0.00835, 0.21726,
+ 0.14734, -0.37381, -0.14563, -0.28266, -0.11238,
+ -0.43409, -0.18221, -0.29650, 0.15123, 0.07206,
+ -0.22893, -0.04378, -0.54708, -0.09525, -0.01850,
+ 0.29831, 0.14338, -1.15739, 0.35316, 0.19144,
+ -0.67234, 0.22700, -0.25903, -0.62579, 0.26500,
+ -0.04329, 0.51701, -0.54270, 0.93665, 0.15567,
+ -0.11653, 0.55251, -0.12562, -0.35038, -0.15960,
+ 0.05972, -0.89357, 0.52445, 0.24884, 0.32836,
+ 0.10950, -0.76283, 0.18871, 0.13661, -1.82029,
+ 0.36462, -0.66394, 0.02112, -0.44600, 0.22614,
+ 0.76964, -0.59718, 0.32372, -0.32791, -0.44381,
+ 0.73030, 0.16270, -0.32026, -0.28157, -0.17087,
+ -0.75360, 0.65118, 0.27943, 0.17649, 0.60209,
+ -0.73677, 0.28705, -0.56113, -0.31276, -0.61527,
+ 0.06015, 0.12466, 0.01469, 0.18450, -0.36192,
+ 0.23525, -0.26764, 0.02324, 0.05242, 0.70723,
+ -0.75031, -0.32730, 0.28744, -0.07167, 0.00446,
+ -0.19506, -0.30414, 0.25019, 0.34592, -1.01082,
+ -0.31368, -0.41940, -0.61653, -0.37505, -0.47662,
+ 0.16582, 0.57373, -0.45601, 0.19505, 0.08073,
+ -0.17274, 0.01899, 0.06667, -0.31084, 0.05406,
+ -0.05983, 0.28434, -0.75648, 0.22401, 0.25674,
+ 0.20713, -0.39621, -0.79014, 1.12186, 0.39844,
+ -0.19126, 0.42704, -0.28623, -0.05127, -0.19098,
+ -0.28229, 0.21678, -0.61366, -0.16859, -0.46302,
+ 0.33301, -0.01064, -0.49309, 0.05424, 0.52616,
+ -1.00615, 0.37081, -0.41379, -1.60893, 0.04804,
+ 0.07036, -0.22229, -0.11848, 0.09449, -0.18469,
+ 0.06638, -0.08913, 0.07839, 0.04583, -0.15725,
+ -0.10083, -0.07341, -0.10724, -0.17542, -0.09354,
+ -0.09185, -0.15581, -0.11566, 0.08076, 0.06650,
+ 0.07584, -0.13234, -0.11164, 0.10893, -0.13442,
+ -0.14392, -0.09000, 0.09434, 0.07486, 0.05751,
+ -0.19902, 0.08123, -0.09441, -0.10340, 0.01171,
+ 0.01233, 0.04941, -0.09055, -0.14678, 0.05831,
+ 0.08638, 0.09109, 0.05060, -0.06253, 0.10451,
+ 0.06364, 0.05428, -0.09793, -0.08119, 0.06769,
+ 0.03185, 0.02677, -0.12090, 0.01664, -0.02800,
+ -0.13372, -0.14904, -0.15843, -0.04911, 0.08312,
+ 0.07699, 0.07749, 0.05901, 0.02435, -0.06695,
+ 0.08127, -0.08123, -0.04937, 0.09272, -0.10459,
+ -0.08984, -0.12323, 0.05026, -0.12970, 0.09023,
+ 0.03396, -0.14183, -0.13230, -0.11571, 0.11119,
+ 0.06370, -0.17914, -0.12896, -0.11717, 0.06979,
+ -0.07790, 0.08053, 0.07503, 0.05526, 0.07236,
+ -0.11131, 0.05448, 0.05178, -0.04607, -0.10486,
+ 0.03856, 0.09990, -0.14184, 0.11090, -0.20159,
+ -0.08426, -0.05064, -0.16659, 0.05744, -0.14411,
+ 0.04097, -0.19723, 0.10926, -0.13130, -0.19726,
+ 0.08843, 0.14221, 0.06845, 0.05881, -0.09851,
+ 0.11262, 0.09022, -0.18148, -0.13671, -0.00159,
+ -0.12086, -0.10113, 0.06622, -0.06973, -0.13433,
+ 0.08657, -0.14121, -0.16315, -0.08428, 0.09399,
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+ 0.06645, -0.34244, -0.14804, -0.08514, 0.06471,
+ 0.15776, -0.24499, -0.28307, -0.21154, 0.04442,
+ 0.07667, -0.03098, -0.24302, -0.08463, -0.44392,
+ 0.14498, 0.02885, -0.02168, -0.03008, -0.16821,
+ 0.05709, -0.05235, 0.01731, 0.04747, -0.10305,
+ 0.23791, -0.00678, -0.15607, -0.29312, -0.15930,
+ 0.24028, -0.01704, -0.05967, -0.20229, -0.20499,
+ 0.03414, -0.06031, -0.15557, 0.42913, -0.13016,
+ -0.11917, -0.23346, -0.62328, -0.25769, 0.12541,
+ -0.24434, -0.12909, 0.11370, -0.13742, 0.15928,
+ -0.43197, 0.17736, -0.09786, 0.12649, -0.21616,
+ -0.08004, 0.06531, 0.03390, -0.05532, 0.07588,
+ -0.10185, -0.24355, -0.27340, 0.25280, -0.18614,
+ -0.14478, 0.20455, 0.03111, 0.34689, -0.10109,
+ 0.13320, -0.28762, -0.11317, -0.23129, 0.03169,
+ 0.08211, -0.33323, -0.26039, -0.10453, -0.06129,
+ -0.12699, -0.22528, -0.02769, -0.23302, -0.14080,
+ -0.34889, 0.36699, -0.23899, -0.09137, 0.31056,
+ 0.10739, -0.05424, -0.02255, -0.07504, 0.23690,
+ -0.21730, 0.09734, 0.25106, -0.03583, 0.15984,
+ 0.02890, -0.41749, -0.16643, 0.06191, -0.21642,
+ -0.12253, 0.07472, -0.18434, 0.23741, -0.02664,
+ 0.15417, -0.24200, 0.11155, -0.19113, -0.14911,
+ 0.01229, -0.09510, 0.34582, 0.19537, -0.55653,
+ 0.03497, 0.07174, 0.13610, 0.07113, 0.28685,
+ -0.29092, -0.74698, -0.34527, -0.17715, 0.15422,
+ 0.08963, 0.20586, -0.26573, 0.22127, 0.25848,
+ 0.13101, -0.27505, -0.20266, 0.01379, -0.08983,
+ -0.17205, -0.13932, 0.06368, -0.18849, -0.29517,
+ -0.00227, 0.14874, -0.24353, -0.04352, -0.16716,
+ -0.14517, 0.35429, 0.04160, -0.08369, 0.00311,
+ -0.04979, 0.29767, -0.25788, 0.10000, -0.04418,
+ -0.14141, -0.10048, -0.00688, -0.12263, -0.22515,
+ -0.27330, 0.18413, -0.23630, -0.44105, -0.58793,
+ 0.22892, -0.24026, 0.04072, -0.07196, -0.21496,
+ 0.22512, 0.05071, 0.34280, -0.05296, 0.23204,
+ 0.18528, 0.32235, -0.25034, -0.08756, -0.07260,
+ 0.11741, -0.21241, 0.08804, -0.10945, -0.20710,
+ 0.11189, 0.01634, -0.35545, 0.01213, -0.03890,
+ -0.32168, -0.25713, 0.08308, -0.25297, -0.02362,
+ -0.00285, 0.14488, -0.02281, -0.15358, -0.30229,
+ 0.17257, 0.25149, -0.08735, 0.31050, 0.10771,
+ -0.40015, -0.32587, -0.06626, -0.29023, 0.05774,
+ -0.12251, 0.22127, 0.27650, 0.01635, -0.03284,
+ -0.20761, -0.20339, -0.15960, -0.33263, -0.36227,
+ 0.12549, -0.07434, -0.16467, 0.01048, -0.01551,
+ 0.18801, 0.04069, -0.16690, 0.16716, -0.22829,
+ -0.01397, -0.06661, -0.11163, 0.43491, 0.00452,
+ -0.00131, -0.14298, 0.01357, -0.02535, -0.08741,
+ 0.02878, -0.33685, -0.10398, -0.20159, -0.01230,
+ 0.18747, 0.15414, -0.82261, 0.22058, 0.24937,
+ -0.26526, 0.19615, -0.15668, -0.42551, 0.04430,
+ -0.35537, 0.38725, -0.02845, -0.10262, 0.34683,
+ -0.08344, 0.02718, -0.08554, -0.15171, -0.42300,
+ -0.03014, 0.31708, -0.11910, -0.50152, 0.08218,
+ 0.09012, 0.05573, -0.10694, 0.11805, 0.03516,
+ 0.28830, -0.14738, -0.20038, -0.44594, 0.07853,
+ 0.27269, -0.17831, -0.05562, -0.04752, 0.01314,
+ 0.11139, -0.25419, 0.07140, 0.06125, -0.59125,
+ -0.13096, 0.31949, -0.18687, 0.04214, -0.01327,
+ -0.28866, -0.18650, -0.11207, -0.06022, -0.11399,
+ -0.12809, 0.30109, -0.25088, 0.02917, -0.14330,
+ 0.16127, -0.33023, -0.04793, 0.23474, 0.24801,
+ -0.15065, 0.04382, 0.31553, -0.39668, -0.11310,
+ -0.05332, 0.05824, 0.08353, -0.14884, 0.16177,
+ -0.35127, -0.10698, 0.17288, -0.28728, -0.09405,
+ 0.11636, -0.01310, 0.14964, -0.20337, -0.05516,
+ -0.28408, -0.38414, -0.30923, -0.24966, -0.06487,
+ 0.33634, 0.16125, -0.03343, 0.31329, -0.05910,
+ 0.15765, -0.23056, 0.00459, -0.35405, 0.03048,
+ 0.30842, -0.07739, 0.04623, -0.18645, -0.01021,
+ -0.16461, -0.13498, 0.07759, -0.33124, 0.04659,
+ -0.26603, 0.29268, -0.01134, -0.21892, 0.26644,
+ -0.07514, 0.21750, 0.08860, 0.19967, -0.88526,
+ 2.89793, 3.38478, -0.17743, -2.01154, -2.13841,
+ 2.41412, -1.44365, -0.68899, 2.72111, -0.63474,
+ -2.88874, -0.53128, 2.82926, 2.99491, 3.28476,
+ -2.30931, -2.63205, -0.21304, 0.75074, 0.32874,
+ -2.97648, 0.90941, -0.21009, 0.18400, 0.08316,
+ -0.51175, -3.82386, -0.25475, 0.35850, 1.57044,
+ -0.75824, -2.89794, -3.38477, 0.17702, 2.01153,
+ 2.13843, -2.41416, 1.44346, 0.68899, -2.72109,
+ 0.63469, 2.88877, 0.53104, -2.82932, -2.99490,
+ -3.28475, 2.30931, 2.63208, 0.21299, -0.75084,
+ -0.32883, 2.97642, -0.90959, 0.21000, -0.18427,
+ -0.08336, 0.51147, 3.82379, 0.25433, -0.35889,
+ -1.57052, 0.75890
+};
+
--- /dev/null
+float const r19_1[(na*19+1)*30+(30+1)*2] = {
+ -0.95328, -0.77139, -1.60266, 0.41389, -0.55944,
+ -0.09261, 0.36393, -0.81729, 1.13541, -0.53407,
+ -1.88892, 0.09164, 0.23079, 0.71593, -0.09880,
+ -0.35125, -0.03633, 0.81765, -0.62638, 0.33504,
+ 1.14452, -2.55167, -1.44324, -0.23018, 0.63622,
+ -0.42933, 0.27642, -0.74615, 0.01781, 0.61312,
+ 0.62471, 0.41202, 0.89315, 0.00013, 0.29785,
+ 0.62022, -0.08664, -0.48270, 0.42957, -0.84188,
+ -0.96089, 0.06786, 0.11304, 0.06773, -1.21104,
+ 0.07608, 1.47622, 0.24608, -0.17754, 0.20253,
+ 0.79648, -0.94010, 1.72333, 0.69349, 0.88670,
+ -1.07269, -1.59213, -1.21268, -0.93639, -0.26167,
+ -0.48366, -0.83667, -0.44077, 0.28514, 0.22241,
+ -0.24138, 0.37517, -1.68549, 0.42590, 0.53219,
+ -0.16361, -0.54321, 0.57916, -0.42437, -0.99068,
+ 0.03814, -0.35022, -0.00169, 1.15615, -0.05973,
+ 0.40759, -1.23535, -0.43610, -0.77363, -0.59044,
+ -0.91016, -0.92450, 0.20242, 0.51723, -0.50648,
+ -0.59255, 0.26903, 1.38102, -0.23379, 0.04323,
+ -0.64327, 0.36935, -1.49041, 0.85614, -0.60358,
+ 0.72587, -0.45530, -0.94245, 0.71462, -0.06957,
+ 1.36588, -0.02451, 0.48107, -0.13626, -0.60472,
+ -0.24703, 0.61027, 1.17135, -0.37464, -0.20411,
+ 0.02459, -0.55855, -0.41517, -0.74277, -0.66403,
+ -1.31469, -0.10404, -1.00292, -1.24002, -0.23620,
+ 1.13292, -1.47257, 0.20422, -0.85074, -0.69754,
+ -0.24432, -0.25969, -0.85368, 1.01746, 1.02132,
+ -0.12494, -1.05877, -0.58296, -0.40002, 0.07463,
+ -0.02298, -0.31616, 1.11281, -0.82667, 0.22219,
+ 0.25545, 0.51942, -2.50551, -1.03077, -0.23737,
+ -0.38685, -1.08324, -0.60473, 0.09869, 1.06330,
+ 0.55966, 1.04008, 0.05067, -0.08920, -0.43510,
+ -0.32209, -0.95778, 0.02048, 0.27753, 0.40670,
+ -0.03943, 0.37983, 0.51151, 0.07237, 0.28651,
+ -0.07987, -0.62851, -0.58883, -1.47715, -0.28897,
+ 0.22959, 0.00554, -1.13838, -0.13678, 0.33454,
+ 0.11433, -0.37457, -0.28593, -0.26160, -0.10894,
+ -1.22883, 0.46694, 0.05492, 1.54998, -0.41932,
+ -1.04839, 1.51988, -0.12487, -0.09853, -1.03458,
+ -1.60599, -1.00074, 0.73652, -0.98487, -0.49967,
+ 0.60341, -0.72671, -0.11477, -0.46963, 0.84170,
+ 0.81679, -0.39636, 0.92879, -0.30635, -0.10000,
+ 0.19009, -0.25941, -0.01443, -1.11245, -0.40830,
+ -0.19309, -0.37386, -0.20790, 0.60883, -0.11218,
+ 0.90098, 0.60737, -0.41109, -0.84890, 0.29156,
+ 0.31997, 0.00974, -0.15058, -0.87214, -1.55439,
+ 0.90654, -0.19233, -1.00619, 0.80204, 0.87487,
+ -0.19975, 0.08537, -0.23437, -0.45987, 0.73241,
+ -0.74409, 0.46260, 0.66040, -1.02208, -0.19424,
+ -1.02447, -1.31748, -0.42324, -0.91888, -0.06904,
+ 1.06243, 0.44226, -0.73063, -1.27364, 0.34482,
+ 0.15803, -0.65204, -0.88884, -0.55985, 0.59768,
+ -2.08460, -0.51715, 0.53015, -1.03666, -0.34511,
+ 0.31531, 0.84166, 0.55253, 0.64809, 0.69511,
+ 0.27480, -0.01467, 0.26131, -1.03115, -0.56074,
+ -0.86074, 0.92588, 0.09252, 0.23498, 0.05362,
+ 0.34442, -0.18344, 0.68279, 0.42793, -0.04010,
+ -0.64379, -0.03907, 0.81766, 1.24481, -1.69012,
+ -1.58368, -0.90500, -0.52601, 0.55549, -0.99713,
+ -1.00396, 0.11367, -1.50093, 0.58617, -0.62664,
+ -0.34512, -0.41086, 0.02878, -0.37524, 0.24501,
+ 0.33535, 0.24397, 0.38697, 0.42469, -0.22223,
+ 0.25943, -0.53243, 0.61816, -0.37073, 0.05939,
+ -1.71852, -0.55987, 0.31273, -1.06344, -0.26746,
+ -1.03846, -0.47070, 0.06270, -0.60021, -0.05799,
+ -0.24107, 0.75954, -0.52818, 0.17529, 1.52097,
+ 0.92512, 0.39887, -1.25488, 0.05931, 0.57279,
+ 0.12984, 0.25096, -1.71095, 0.82626, 0.23251,
+ -0.86307, 0.11689, 1.12203, -0.89706, 1.42879,
+ -1.32525, -0.32001, 0.18618, -1.65563, -0.39044,
+ 0.46399, -0.16602, 0.15557, -1.24943, 0.84134,
+ 0.29281, -0.02326, -0.57811, 0.09593, -0.85305,
+ -0.63830, -0.50456, -0.40173, 0.67572, 0.02871,
+ 0.75864, -0.13198, -0.22016, -0.34374, -1.30400,
+ 0.88204, -0.03098, -0.40538, -0.09756, -0.51972,
+ 0.72696, 0.44912, -0.27148, 1.28098, -1.13289,
+ 0.51606, 0.63691, -0.49528, 0.14124, -0.24386,
+ -0.75684, -1.31928, -0.03695, 0.72832, -0.45410,
+ 0.72426, -0.13996, -0.87914, -0.15406, -0.61668,
+ -0.92935, 0.61985, -0.18728, 0.21439, -2.88436,
+ 0.65266, -0.69433, -0.74843, -0.08504, -0.67191,
+ 0.48298, -0.75868, 1.39851, 0.07226, -0.76191,
+ 0.63583, -0.62077, -0.64022, 0.14935, -0.35289,
+ -0.41629, -0.52878, 0.03460, 0.89445, 0.04403,
+ -0.63489, -0.12601, -0.03803, 0.23009, 1.39375,
+ -0.12753, 0.04294, 0.62530, -0.37115, 1.53684,
+ -0.16585, -0.07138, -0.83322, -0.31276, 0.19560,
+ -1.46169, -0.81690, -0.58565, -0.30630, -0.26093,
+ -1.08216, -0.61445, -0.27948, -1.32954, -0.37721,
+ 0.97592, -0.91503, -0.02921, 1.35278, 0.33156,
+ -0.00120, 0.14000, -0.16020, -0.86874, -0.07473,
+ -0.13179, -0.77978, -0.31657, 0.00307, 0.03686,
+ -0.11716, 0.53781, 0.65316, -1.20919, 0.22846,
+ -0.32091, 0.65046, 0.63880, 0.56358, -0.13894,
+ -1.46361, 1.17058, 0.28416, -0.05373, -0.75136,
+ -0.72516, 0.56023, -0.64532, 0.15121, -0.12761,
+ -1.91172, -0.18239, 0.42900, -0.29596, 0.42607,
+ -0.65056, 0.71688, -0.53235, 0.60066, 0.50614,
+ 0.54688, 0.63328, 1.10000, 0.16929, 0.08169,
+ -1.39178, 0.19652, -0.33284, -0.91257, -0.69508,
+ -0.97309, 0.45402, -0.45541, -1.16628, -0.47093,
+ -0.41783, 0.49072, 0.62950, 0.06753, 0.93745,
+ 0.80589, 0.16802, -0.11953, 1.54497, 0.55143,
+ -0.11193, -1.71351, -0.65530, -0.51668, -1.22368,
+ -0.01408, -0.62418, -1.14616, -0.50783, -0.24330,
+ -0.65104, 0.28273, -1.46035, 0.07558, -1.89386,
+ -0.34970, 0.88386, 0.33048, 0.11108, 0.62632,
+ 1.13362, 0.42480, -1.06916, 0.92821, -0.27221,
+ -1.05191, -0.38028, -0.29454, -0.25586, 0.29792,
+ -0.06040, -0.35582, 0.62012, 1.27041, -0.31701,
+ -0.65042, 0.23083, 0.85535, -0.24480, -1.28873,
+ -0.49143, 1.58878, 0.98960, -0.03234, 0.08993,
+ -2.12761, -1.11982, 0.71584, -0.67110, -0.46632,
+ 0.06653, -0.70075, -0.46655, -0.19755, 1.81724,
+ -0.16081, 1.58574, 0.87189, 2.97636, 1.69702,
+ -1.31415, 1.53461, 0.99378, -0.49157, -1.52578,
+ -2.17660, -0.13561, -1.33028, -2.39955, -2.01665,
+ -1.02627, -0.22844, -0.27087, -0.35195, 0.33656,
+ -0.19288, 0.24597, 0.10770, 0.90857, 1.33074,
+ 0.78836, 0.18768, -0.11260, 0.15908, -0.75019,
+ -0.64011, 0.12263, -0.15650, -2.00916, -1.38266,
+ 0.05227, 0.40453, -0.57374, -0.67582, 0.10000,
+ -0.45220, 0.61852, -0.27329, 0.16768, -0.65699,
+ 0.62891, -0.25517, -0.38625, -0.29049, 0.72535,
+ 0.02459, 0.64585, -0.52527, -0.62522, -1.01303,
+ -0.65382, -0.16045, 0.70619, -0.56990, 0.29303,
+ -0.49753, 0.52185, 1.45135, 1.13085, -1.62513,
+ 1.43968, 0.40695, 0.08432, -0.45464, -0.45263,
+ 0.85717, 0.80184, 0.10062, 0.93036, -0.80256,
+ -1.66828, -1.15773, -0.76987, -0.16793, -1.21664,
+ -1.16073, -0.39835, -0.86523, 1.19089, 0.49973,
+ 1.23450, 0.32312, 0.78550, -0.08500, 0.57010,
+ 1.60162, 0.26065, 0.18845, -1.09420, -0.85546,
+ 0.07758, -2.03839, -1.34401, -0.04124, -0.16684,
+ -1.22698, -2.01122, -0.55299, 0.16671, -0.70361,
+ 0.14236, 0.77800, 0.19144, 0.14148, 0.20730,
+ -1.60585, 0.23227, 0.72272, -0.82882, -0.47305,
+ 0.65833, 0.43641, -0.77815, -0.02037, 0.24274,
+ 0.01227, -0.87280, -0.59225, -0.60665, -0.84922,
+ -0.97239, 0.03664, -1.24431, -0.02363, -0.64290,
+ -0.71940, 0.52266, 0.31038, 0.09192, -0.69937,
+ -0.66300, 0.77104, 0.23540, -0.36393, 0.13081,
+ 0.36494, 0.87768, -0.32297, -0.49988, 0.31005,
+ -0.33815, 1.05010, 0.62242, -1.15911, 0.17711,
+ 0.95761, -0.06740, -1.30682, 0.63107, 0.80945,
+ 0.18403, -0.97429, 1.39121, -0.11881, -0.35995,
+ -1.07552, -1.75436, 0.02419, -0.20841, -1.97811,
+ -0.05574, -0.01952, -0.46808, -0.00497, 0.37103,
+ -1.47588, 0.87290, 0.58554, 0.79257, -0.99885,
+ 0.79012, -0.65832, -0.17497, -0.51183, -0.84113,
+ -0.89356, -0.31608, 0.34545, 0.45662, 0.02922,
+ -0.70568, -0.72404, 0.21084, 0.34858, -0.99201,
+ -0.31449, 0.70091, -0.43550, -0.58558, -0.22295,
+ 0.31398, 0.02036, -0.10991, -1.30162, 0.82355,
+ -0.36524, -0.60215, 0.23891, -0.67519, -0.02419,
+ -0.15127, 0.30970, -0.53620, -0.63424, 0.09794,
+ -1.43363, 0.45155, 1.01774, -0.23768, -1.17500,
+ 0.58761, 0.98174, 0.46963, -1.11931, -0.69253,
+ 0.03793, -0.05398, -1.48158, 1.14678, 0.50827,
+ -1.33037, 0.43264, 0.60369, -0.92664, -2.54953,
+ -0.02093, 0.00394, 0.06288, -0.27211, 0.61791,
+ 0.40179, 0.31444, 0.54843, 0.95010, 0.04952,
+ -0.92524, -0.58770, -0.03010, -0.08691, -0.99167,
+ -0.13883, -0.63617, -0.08737, -1.56141, 0.25877,
+ -0.66494, 0.19839, -1.39419, -0.88835, -0.56372,
+ -0.44662, -0.18256, -0.26213, 0.74956, -0.95897,
+ 0.47020, -0.90919, 0.49579, 0.33746, 0.17626,
+ -1.38634, -0.65841, 0.25109, 0.32711, 0.70877,
+ 0.24097, 0.69945, -0.54910, -0.51800, -1.03629,
+ -0.84999, 0.97963, -0.54011, -0.39321, -0.43210,
+ -0.49560, -0.11805, -0.27118, -0.19464, 0.86800,
+ -0.27057, -1.14093, -0.73955, 0.68970, 0.64921,
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+ 0.55861, 0.84083, 0.25558, -0.72474, -0.26765,
+ -0.44190, 0.52570, 0.58112, -0.07261, -0.03192,
+ -0.03516, 0.23422, -0.78305, 0.27145, 0.48867,
+ -0.09520, 0.07154, -1.32722, -0.96830, -0.56809,
+ -0.89538, 0.14511, 0.45164, 0.89453, -0.61245,
+ -0.76614, -0.55812, 0.75713, 0.86205, 0.36539,
+ 0.41027, 0.18456, -1.01041, -0.40846, -1.99558,
+ 0.09323, -1.03438, -0.64954, -0.17405, -0.73682,
+ 0.06436, 0.05206, 1.64403, 0.67028, -1.45601,
+ 0.39566, -0.50172, -0.38173, -0.67427, -0.44126,
+ -0.25231, -1.55484, -0.00254, -1.29437, -0.99488,
+ -1.02758, 0.00012, -0.71397, -0.24179, 1.47732,
+ -0.97118, 0.64777, -0.43074, 0.17827, 0.51614,
+ 0.30446, 1.17554, 1.12972, 0.52077, 1.18206,
+ -0.85009, 1.43093, -0.07408, -0.36939, 1.41553,
+ -0.72762, -1.33543, 0.72878, -0.10008, -0.05437,
+ -0.01555, -0.31782, -0.13535, -1.97759, 0.31865,
+ -0.59947, -1.52586, 0.19655, -0.73946, -0.10000,
+ -0.83634, -1.19004, 0.87871, 0.05372, -0.75811,
+ -0.53424, 0.09727, 0.55873, -0.77830, -0.14339,
+ 0.72470, -0.45502, -1.36653, -0.58629, -0.96495,
+ 0.52971, 0.66838, -0.04062, -0.12684, -0.63682,
+ 0.45668, -0.20602, -0.24232, -0.37487, -0.59655,
+ -0.84158, -0.03457, -0.25107, -0.01818, 1.43426,
+ -0.15838, 0.57464, -0.57376, -0.68327, 0.17396,
+ 0.46188, 0.02445, -0.20928, -0.40542, -0.26310,
+ -0.59761, -0.06290, -1.14488, 0.23088, -1.12828,
+ -0.18092, -0.19212, 0.71760, -0.54489, -0.39531,
+ -0.05248, 0.47622, 1.40726, -0.34303, -0.41498,
+ 0.10446, 0.44194, -0.69547, 0.64351, -2.58649,
+ 0.58536, -0.66567, -0.11246, -2.08740, -0.25871,
+ -0.61847, -0.31843, -0.26528, -0.33771, -0.07144,
+ 0.10883, -2.38947, 0.35323, -0.47582, 0.46016,
+ 0.13975, 0.19190, 1.83514, 0.10299, 0.82099,
+ -0.22899, 0.51762, 0.17983, -0.30842, -0.73721,
+ -0.84255, 0.27817, -0.48514, -1.92614, 0.97500,
+ -1.17947, -0.29729, -0.20747, 0.35112, 0.06775,
+ 0.70958, -0.96108, -0.35789, 1.06233, 0.52919,
+ -0.79791, -0.69004, 0.38913, 0.63631, -0.36608,
+ -0.95778, -0.24504, 0.02187, 0.19066, 0.28554,
+ 0.33559, -0.15682, -0.56685, 0.73815, -0.00666,
+ -0.47532, 1.23357, 0.79296, 0.43744, -1.39314,
+ -0.76125, -0.54470, -0.56116, -0.28555, -0.66421,
+ -0.86692, -0.03594, 0.50152, 0.25299, 0.20179,
+ 0.95385, -1.41389, -0.89964, 0.11179, -0.05221,
+ -1.06727, -0.63241, 0.40852, -0.82848, 0.33021,
+ -0.16002, -0.37191, -0.00218, 0.48793, 0.50869,
+ -0.59625, -1.14677, 1.23501, 0.51867, -0.62752,
+ 0.42515, 0.18199, -0.58886, -0.87795, -0.46679,
+ -1.20201, -1.15440, -0.34034, 0.79845, 0.83182,
+ 0.05484, -0.93751, 0.18782, -0.42595, -0.74077,
+ 0.48743, 0.06303, -0.67172, 0.02109, 1.50509,
+ 0.34406, -1.14993, 0.43463, 0.42138, 1.14039,
+ 0.46000, -0.71452, -1.10819, -1.37945, -1.15451,
+ -0.11654, -0.03398, -0.67678, -0.61446, -0.45661,
+ 0.32687, 0.01435, -0.18971, -0.52281, -3.24991,
+ 0.57508, -0.67539, -0.36570, 0.36291, -0.35894,
+ 0.23622, 0.70482, -1.13125, -0.46299, 0.64017,
+ -0.27433, 1.02703, -0.10478, 0.10932, -0.02998,
+ -1.14104, -0.46454, -1.73139, 0.08023, -0.09030,
+ 0.31530, 0.42428, -0.21686, 1.15978, 0.43892,
+ 0.22902, -0.35986, -0.74785, 0.58290, -1.72378,
+ 0.14795, -0.34551, 0.01195, 0.42903, -0.09394,
+ -0.43069, 0.12190, -0.58494, -0.48669, -1.66750,
+ -0.70390, 1.03624, -0.83231, 0.44024, 0.54959,
+ 0.98648, -0.51197, 0.67074, -0.54772, 0.18977,
+ 0.27117, -0.93352, -0.03403, 0.19260, -0.50097,
+ -0.31974, -0.86872, -0.85905, -0.51327, -1.00820,
+ -0.15319, 0.36326, -0.16068, 0.15762, -0.13906,
+ 0.03544, 1.06940, -0.75239, 0.16460, -0.75985,
+ -1.63865, -1.26505, -0.60181, -1.15870, 0.57658,
+ 0.86769, -0.19283, -0.05490, 0.65113, 0.05478,
+ 0.17153, -0.23137, 0.18963, -0.52334, -0.57669,
+ 0.67885, 0.23926, -0.84923, 0.79629, -0.23526,
+ -0.99287, -0.79606, 0.89969, -1.59481, 0.02903,
+ -0.42338, 0.60436, 0.04054, -0.47020, -0.51222,
+ 0.21973, -0.63699, 0.43159, 0.40849, 0.16031,
+ 0.84285, 0.89900, 0.74529, -0.62960, -0.76602,
+ 0.33673, 0.86943, -0.70009, 0.82248, -0.92861,
+ -1.00205, -0.18977, -0.49961, 0.74008, -0.11361,
+ -0.69892, -1.54510, 0.24136, -0.39031, -1.32087,
+ -0.29221, -0.03454, 0.43269, -0.27603, 1.42624,
+ -0.58757, 0.25131, -0.20137, -0.22223, 0.38929,
+ -0.36132, -0.95123, -0.20204, -1.10945, 0.46250,
+ 0.46132, -1.55821, -1.27437, 0.50874, -0.41630,
+ 0.54620, -0.66322, 0.71058, 1.22225, 0.67198,
+ 0.73467, 0.89237, 0.51884, 1.40309, -2.22003,
+ -0.52175, -0.89210, -0.74544, -0.86106, -0.43792,
+ -1.35376, 1.05050, -0.54782, -1.60868, 0.06198,
+ 0.14483, -0.66976, -0.13233, -0.50164, 0.63996,
+ 0.06938, -0.28174, 0.23031, -0.62621, -0.83175,
+ -1.12857, -0.68409, -0.73048, -1.00664, 0.34272,
+ 0.42781, -0.09535, 0.29012, 0.08677, 0.38090,
+ 0.08177, -0.61830, -0.31978, 0.89528, -2.08040,
+ -0.48174, -0.66853, -0.49759, -0.60226, -0.21588,
+ 0.38184, -1.92249, -1.05349, -0.13554, -0.45327,
+ 0.17165, 0.10528, -0.64463, 1.12161, 2.07275,
+ 0.55867, -0.48767, 0.20472, 1.74747, -0.10000,
+ -0.22818, -0.40233, -0.33488, -0.17399, -0.25022,
+ -0.18392, -0.21854, -1.58830, 0.18791, -1.16106,
+ 0.82543, -0.56034, -0.02062, -0.16850, 0.17723,
+ 0.13301, -1.28724, 1.12280, 0.20074, 0.50727,
+ 0.44412, -1.06506, -0.42332, -0.00608, 0.83993,
+ 0.04749, 0.07912, 1.03500, 0.31536, 0.41793,
+ -0.61907, 0.02014, -0.30654, -1.47032, -0.01563,
+ 0.40941, 0.49523, -0.86193, -1.96530, -0.45713,
+ 0.11553, 0.23574, -0.13494, 1.15648, -0.16056,
+ -0.84608, 1.30830, 0.64833, 0.30241, -0.37471,
+ -0.57335, -0.20163, 0.24080, 0.06658, -1.83220,
+ -0.07888, 0.31524, -0.73571, -1.67774, -0.25440,
+ 0.71907, -0.38314, -0.28344, 0.72418, 0.50463,
+ -1.00796, 1.40379, 0.32410, 0.03878, -0.84369,
+ -0.67265, 0.48023, -0.00307, -0.03299, -0.55747,
+ -1.06732, -0.04998, -0.07294, 0.48355, -0.03881,
+ -0.59990, -0.29415, -0.55966, -0.93819, -1.59813,
+ -1.17118, 0.21003, -0.01278, -1.23067, -0.46515,
+ 1.67217, -0.43317, -1.94603, 0.64138, -1.36924,
+ 0.10593, 0.16810, 0.37019, 1.27305, 0.25538,
+ 0.86949, 0.02806, -0.09841, 0.42306, -0.47163,
+ 0.12069, -0.39077, -0.19143, 0.26774, -1.99036,
+ 0.22977, 0.02579, -2.07159, -2.04508, 0.56842,
+ -0.28854, -0.44762, -0.88466, 0.10739, 0.65469,
+ 0.53234, 0.01376, 1.11417, -0.43111, 0.26226,
+ 0.46459, -0.20384, -0.11394, -1.33273, 0.01645,
+ -1.06480, 0.37883, -0.28382, -0.77645, -0.71136,
+ -0.45862, 0.58615, -0.33798, 0.00445, 0.26092,
+ 0.29135, 0.27170, 0.24658, 0.91781, -0.61944,
+ -0.81189, -0.03896, -0.65714, -0.64585, 0.30190,
+ 0.85442, 0.87167, -0.61090, -0.67379, -0.41398,
+ -0.98689, 0.33865, -0.69181, 0.35663, 0.48691,
+ -0.74787, 0.44396, 0.25514, -0.74119, -0.05919,
+ 0.02238, -1.04268, 0.36009, 0.14384, -0.25931,
+ 0.39756, 0.47902, 0.67417, -0.65112, -0.09488,
+ -0.37597, -0.26202, -0.67679, -1.70326, 0.79791,
+ -0.57494, -1.40930, -0.76754, 0.55271, 0.22214,
+ -0.43516, 0.49717, 0.28643, -0.22024, -2.98015,
+ 1.53575, -1.14424, -1.61750, -2.10727, 1.54394,
+ 1.67639, -1.90906, 2.10356, -1.60554, 1.03786,
+ 1.98557, -1.37494, -1.43206, -1.49549, -1.89654,
+ 1.48550, 1.40159, -1.55168, -1.70671, 1.38930,
+ -2.19847, 1.35406, 1.25543, 1.50491, 1.17142,
+ 1.43774, 1.69917, -1.65321, 1.33468, 1.79461,
+ -0.12524, -1.53577, 1.14423, 1.61750, 2.10727,
+ -1.54393, -1.67638, 1.90907, -2.10356, 1.60554,
+ -1.03786, -1.98558, 1.37495, 1.43205, 1.49549,
+ 1.89654, -1.48549, -1.40158, 1.55168, 1.70670,
+ -1.38930, 2.19847, -1.35407, -1.25543, -1.50491,
+ -1.17143, -1.43774, -1.69916, 1.65320, -1.33468,
+ -1.79461, 0.12523,
+};
+
+float const r19_2[(na*19+1)*30+(30+1)*2] = {
+ 0.08091, -1.00558, -1.98437, -0.53243, 0.51790,
+ 0.23565, 0.64448, 1.19528, -0.54581, -1.24374,
+ -0.07050, 0.03711, -0.24224, -0.34775, -1.07314,
+ 0.50923, -0.28897, 0.28740, 0.30792, 1.42146,
+ -0.51201, -0.93162, -0.07547, 0.45806, -0.06441,
+ 0.43978, -0.77372, -0.66834, 1.18852, 0.64299,
+ -0.11976, -0.40176, 0.44780, -0.50255, 0.57420,
+ 0.12088, -0.85365, -0.74565, -1.20391, -0.18925,
+ 0.27363, -0.02491, -1.05646, -0.31875, 0.01245,
+ -0.63883, -1.34332, -0.88697, -0.48211, 1.87276,
+ 0.39063, 1.10418, 0.04543, 0.15301, -0.21580,
+ -0.63548, -0.60218, -1.16649, 0.20476, 0.51408,
+ 0.31640, 0.54793, -0.22442, -0.70783, -0.88904,
+ -0.95798, 1.23710, -2.13439, 1.21288, 1.55005,
+ 0.61498, -1.25469, -0.18647, -0.34803, -1.23907,
+ 0.22226, -0.04493, -0.32848, 0.64417, -0.77262,
+ 0.75832, 0.28200, -0.33469, 0.26732, 0.24890,
+ -1.18210, -0.95298, -1.38484, -0.82918, -1.15996,
+ 1.34281, 0.12052, 0.96690, -0.79744, 0.92604,
+ 0.17696, 1.23462, -1.00050, -0.28076, -1.76449,
+ -0.54468, 1.31601, 0.02830, 0.51196, 0.61475,
+ -0.09499, 0.07654, -0.52878, -0.42154, 0.12916,
+ 0.20700, 1.16850, 0.42141, -0.35319, -1.62405,
+ 0.75681, 0.43452, -0.31484, -0.40864, -0.53587,
+ -0.06939, -0.59386, 0.59783, -1.34253, -0.35269,
+ 0.23949, 0.17693, -0.11743, -1.20595, -0.05795,
+ 0.18008, -0.30918, -0.02312, 0.71474, -0.72121,
+ 0.12304, -0.03037, -0.33213, -1.14933, 0.31896,
+ -0.48192, -0.37897, 0.46734, -2.14363, -0.70424,
+ 1.30628, 1.55891, -1.03367, -0.88518, -0.12238,
+ -0.43274, 0.00575, -0.49295, 1.22849, 0.90462,
+ -1.72602, 0.05790, -0.91119, -0.34522, 0.54240,
+ -1.00783, 0.51044, -0.35674, -0.84063, 0.16709,
+ 0.00770, 0.22570, 1.69529, -0.75000, 0.15317,
+ 0.02573, -1.24404, 0.07712, -0.36937, 1.80919,
+ 1.59336, -1.64337, -0.70973, -0.14996, 0.23405,
+ 1.46709, -0.37888, 0.01837, -2.34751, -1.16863,
+ -1.53783, 0.74524, -0.46102, 1.62771, -0.76544,
+ 0.21247, 0.40513, -0.09341, 1.51216, 0.71737,
+ 0.79962, -1.42953, 0.23482, -0.08902, -0.69401,
+ -1.93617, -1.56855, -0.49863, 0.56988, 0.19775,
+ -0.17543, -1.33446, 0.77061, 0.25571, -0.10000,
+ 0.67595, 0.30221, -0.17627, 0.19859, 0.55168,
+ -0.68837, 1.11268, -0.02247, -0.12844, -0.80322,
+ 0.67410, -1.14966, -0.43383, -0.19861, 0.29137,
+ -0.38503, -0.26294, 0.48534, -0.63575, -3.04916,
+ 1.43270, -0.13423, -0.88849, 0.48160, 0.22262,
+ 0.37724, -0.44246, 2.05248, -0.46370, -1.12100,
+ -1.56595, -0.81742, 0.22877, 0.48237, -0.27806,
+ 1.77061, -1.08838, -1.00190, -1.35301, 0.29668,
+ -0.03199, 1.06508, -0.29368, -0.17122, 0.37765,
+ 0.33069, 0.48056, -1.27749, 0.92090, 1.08993,
+ -3.21338, -0.39033, 1.26216, 0.30388, -0.28420,
+ -0.09229, -0.51331, -0.73450, -0.58981, 0.38092,
+ -0.50684, 0.16636, 0.34476, -0.08054, 0.11589,
+ -0.68392, 0.42102, 0.78950, -1.10793, 0.27522,
+ 0.97600, 0.70495, -0.57530, 0.31094, -0.36258,
+ -0.09512, -0.05331, -0.10909, 0.25975, -0.69851,
+ -0.02827, -0.70754, -0.97792, -0.58241, -1.00112,
+ -0.61829, 0.24274, -0.35248, 0.45373, -0.86151,
+ 1.24257, -1.07026, 0.30836, -0.94956, -1.34556,
+ 0.59912, 0.22310, 0.25638, 0.26407, 0.34420,
+ 0.11010, -1.32807, 0.56270, 0.43805, -0.12749,
+ -0.66211, 0.03022, -0.18797, -0.16081, 0.18690,
+ -0.56835, 1.27835, -0.20561, 0.11837, 0.91013,
+ -0.39110, 0.52208, -0.83397, -0.53131, -0.15150,
+ 0.36104, -1.69258, 0.02136, -0.46519, -0.85248,
+ 0.86532, -0.70584, -0.79095, -0.22439, 0.17536,
+ -0.57066, 0.38475, 1.68165, 0.54217, -1.33439,
+ -0.01904, -0.50467, -0.90931, -0.45290, -0.64409,
+ 0.07479, -0.16473, 0.18510, 0.29643, -0.23942,
+ 1.15105, -0.14010, -1.94393, -0.17141, -0.64152,
+ 1.74228, 0.54020, -0.70391, 1.54650, -0.24406,
+ 0.32218, -1.36228, -0.17670, -0.14886, -0.05578,
+ 0.07615, 0.08274, 0.06585, 0.25966, -1.49082,
+ -0.24386, 0.31912, 0.01924, 0.53292, 0.22138,
+ -0.29659, -0.44495, 1.02001, -0.71599, 0.36018,
+ -1.06442, 0.64684, -0.46246, -0.37161, -0.77969,
+ -1.53385, -0.04272, 0.52403, 0.03247, -0.54610,
+ 0.02703, 0.66923, -0.93059, 1.14573, -2.40970,
+ 0.59099, -0.69446, -0.75161, -0.20115, 1.28739,
+ -0.52232, -0.54611, 0.51895, 0.66036, -0.76164,
+ -1.01223, -0.48558, -0.32847, -1.00126, -0.65156,
+ -0.33673, 0.63188, 0.58816, 0.22992, -0.66689,
+ 0.38169, -0.05060, -0.55117, 1.02107, -0.84800,
+ -0.92922, 0.65481, 0.42381, 0.65818, 1.01202,
+ -0.02849, -0.88468, -0.08338, -2.38430, -0.57393,
+ -1.36254, -0.06185, -0.14118, 0.86874, 0.58996,
+ -0.49674, -0.50308, -0.68402, -0.79135, -0.00071,
+ 0.28664, 1.10575, 0.89215, 0.19510, 0.09795,
+ -0.03254, -0.94162, -0.48273, 0.15555, 1.55684,
+ -0.82344, -1.33479, -0.97989, 0.02121, 0.35059,
+ 0.25927, 0.16805, -0.88876, 0.29269, -0.39517,
+ 0.43427, 1.04911, -0.11121, 0.19705, -0.07911,
+ -0.04475, 0.73925, 0.37037, 0.55636, -2.10618,
+ -0.80812, -0.10689, -2.20088, 0.01214, -0.14540,
+ -0.89987, -0.31942, -0.38945, 0.28459, -0.95532,
+ 0.66889, -0.13435, 0.74293, -0.10304, 1.06324,
+ -0.22232, 0.72693, 0.58567, 0.14422, -1.18625,
+ -0.14439, -1.05741, -0.13283, -2.01215, -0.89692,
+ -1.22032, 0.66530, -0.34457, 0.59858, 0.54341,
+ 0.74742, -0.15895, -0.28274, -0.20106, 0.45534,
+ 0.70977, 0.16191, -0.61086, -0.31621, 1.80723,
+ -0.95841, -0.14630, -0.44055, -0.15120, -0.51374,
+ -1.53742, -0.42832, -1.06537, -0.37450, -0.53324,
+ 0.56653, 1.10013, 0.54888, 0.72710, -1.05598,
+ -1.37515, 0.64584, 0.30051, -0.58474, 0.75644,
+ -1.41847, -0.81332, 0.21664, 1.12672, 0.20300,
+ -1.39094, 0.07921, -1.00653, -0.01927, -1.39710,
+ 0.96517, -0.47882, 1.15717, 0.62423, 0.15822,
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+ 0.16894, 0.54565, 0.24775, 0.50116, 1.38771,
+ 0.75657, 0.56260, 0.34288, 0.31464, -0.06673,
+ -1.86639, -0.11529, -0.75297, -0.35631, 1.18403,
+ -1.41404, 0.52393, 0.65358, 0.49376, -1.07103,
+ -0.68593, 0.46183, 0.35910, -0.22904, -0.60641,
+ 0.83035, -1.11009, -0.19847, -1.92118, 0.30885,
+ 0.03317, 0.80334, -0.58186, -0.28446, -0.83545,
+ 0.89110, -1.62247, -0.87645, 0.18785, -0.11770,
+ -1.10702, -0.44836, -0.29846, 1.02774, -0.27683,
+ 0.45762, 0.72372, -0.34403, -0.66106, -0.03492,
+ -0.35395, -0.00537, 0.75152, -0.15385, -0.57093,
+ -0.97711, -0.15553, 0.59110, -0.83021, 0.23811,
+ 0.75832, -0.24593, -0.36738, 0.63679, -0.24228,
+ -0.21744, -1.13321, 0.59985, 0.43509, -0.63082,
+ -1.92305, 0.41507, -0.46592, 1.03048, 0.23879,
+ 0.37867, -0.59202, 0.24485, -0.43721, -0.24612,
+ -0.26978, 0.02207, -0.29711, -0.29995, 0.69614,
+ -1.00416, 0.05204, -0.13740, 0.56754, 0.29342,
+ -0.30545, -0.99175, 0.01437, -2.33375, 1.59794,
+ 0.79737, 0.13256, -0.70838, -0.99147, -0.04012,
+ -0.30696, -1.39192, -0.17477, 0.29818, 0.16574,
+ 1.65740, -0.68611, -0.74251, 0.30301, -0.42474,
+ -0.74536, -0.71734, -0.98070, 0.48704, -0.58324,
+ 1.04347, -0.01954, 1.07566, 0.73635, -0.35799,
+ 0.06039, -0.98485, -0.32542, 0.65304, -2.25873,
+ 0.97248, 0.00709, 0.57297, -0.23788, 0.30728,
+ -1.25983, -0.01986, -0.12156, -0.41576, -0.73159,
+ -0.61705, -0.64391, -0.34041, 0.67456, 0.68468,
+ -0.83840, -0.30871, -0.28980, -0.24692, 0.20566,
+ -0.28604, -0.41323, 1.25353, -0.19570, -0.82148,
+ 0.12597, -0.43761, -0.28563, -0.79922, -0.61651,
+ -0.15462, -0.23050, -0.48847, 0.55400, 0.63628,
+ -0.36729, -0.37423, 0.41008, -0.60228, 0.15816,
+ -0.00376, -0.39239, -0.12992, 0.00706, 0.24491,
+ 0.32983, -1.22834, -0.36349, 0.18301, -0.98499,
+ -0.20533, -0.46920, -0.77523, 0.36431, -3.20843,
+ -0.02177, 0.25536, -0.72662, -0.35721, -0.86552,
+ 0.84258, 0.58898, -0.33008, 0.21048, 0.51514,
+ 0.48393, 0.17512, -0.31381, -1.53989, -0.53404,
+ -0.21753, -1.44692, 0.06645, -0.89265, 0.42343,
+ -0.03189, 0.25219, 0.84237, 0.10464, 0.11392,
+ 0.69283, 0.49458, 0.06844, 0.19579, -0.07911,
+ -1.12841, -0.63837, -0.46792, 0.45348, 0.25643,
+ 0.41311, 0.09042, -0.67546, 0.22028, -2.05770,
+ -1.41710, -0.05097, -0.45393, 0.44891, -0.21675,
+ -1.70227, -1.12851, -1.19870, -1.02140, 0.87582,
+ -0.65538, 0.93535, 0.16886, 0.24298, 0.51026,
+ 0.30456, 0.67254, 0.52465, 1.18404, 0.04475,
+ -1.69211, 0.08925, -0.84939, -0.54338, -0.17908,
+ -0.73700, -0.44657, -0.07377, 0.65710, -0.41454,
+ -0.76527, 0.74782, -0.17775, 1.98341, -0.66365,
+ -0.97979, -0.55525, 0.86004, 0.48040, -0.61779,
+ -0.70879, 0.06698, -1.05941, 0.20974, -1.19937,
+ -0.14843, -0.52604, 1.10449, -2.43969, 0.42928,
+ -0.12415, -0.64764, -0.80408, 0.00596, -1.33954,
+ 0.06605, -0.12966, 0.54817, 0.60111, 0.13548,
+ -0.61543, 0.18402, 0.40775, 0.60502, 0.37017,
+ 0.84367, -2.10123, -1.46935, -0.60001, -0.27037,
+ -1.40115, -1.57974, 0.11590, 0.17554, 0.14558,
+ 0.47298, 0.16354, -0.39980, -0.12205, 1.39174,
+ 0.27347, 0.27358, 0.17284, -0.28058, 0.23613,
+ 0.04282, 0.49254, 0.83558, 0.58274, 0.16122,
+ 0.71549, 0.33789, 0.41055, -0.68345, -0.14161,
+ -0.35508, 0.13260, -0.02652, -0.78870, -0.77036,
+ -0.38206, -0.84169, -0.35252, -0.68908, -0.92669,
+ -0.47655, 0.04920, 0.00536, -1.07740, 0.37589,
+ 0.78496, -0.58269, -1.48636, -0.17970, -0.25803,
+ 0.87660, -1.07527, -1.04278, -0.16012, -0.87723,
+ 0.40726, -0.41125, 1.83801, 0.48009, -1.73964,
+ 1.43249, -0.18983, 0.36314, -0.91523, -1.43927,
+ -0.05743, -0.80177, -1.00853, -1.11257, -1.89557,
+ 0.96126, -0.89960, -1.03570, 0.68369, 1.54978,
+ -1.52758, 0.83166, -0.06840, -0.03527, 0.65083,
+ 1.19503, 0.47891, 1.52074, 0.60848, 0.52883,
+ -0.04061, 0.68728, -0.34114, -0.61634, 1.30024,
+ 1.80540, 0.03535, 0.66367, -0.53873, 0.16813,
+ -0.96814, -0.90538, 0.19768, -0.84795, 0.38300,
+ -2.40404, -1.00462, 0.19164, -1.51083, -0.10000,
+ 0.12692, -0.69639, -0.61603, 0.28957, -0.78135,
+ -0.55336, -0.79760, -0.41113, -1.50896, -0.15383,
+ -0.18285, -0.60683, -0.62211, -0.08738, 0.44580,
+ 0.47609, 1.19828, 0.97742, -1.12818, -0.07652,
+ 0.59194, -0.91566, -0.23744, -0.00551, -0.71550,
+ 0.27250, 0.14425, 0.03464, 0.19325, 0.08451,
+ -0.34371, -0.01222, -0.82054, -0.17002, 0.50316,
+ 1.59940, 0.46919, -0.71407, -0.66590, -0.24332,
+ -1.26062, 0.28711, -0.15954, 0.40089, -0.26006,
+ -1.51796, -0.51417, 0.42921, 0.64154, -0.48785,
+ -0.50168, 0.87258, 0.49377, 0.57739, -0.16056,
+ -0.19429, -0.57201, -0.81900, 1.00934, -2.25817,
+ -0.06612, -0.35841, -0.07145, -1.87557, -0.43624,
+ -1.26056, 0.92144, -0.18060, -1.23363, -1.37343,
+ -0.42927, -1.13762, -0.01657, -0.16358, 0.25952,
+ -0.34554, 0.98375, 0.36292, 1.24044, 1.35954,
+ 0.86350, 0.11760, 0.70930, -0.68190, 0.40404,
+ 0.55089, 0.07015, -0.90943, -0.05335, 1.04256,
+ 0.25154, 1.05024, 0.24455, -0.29772, -0.18503,
+ 0.62746, -1.37969, -0.37350, -0.79507, 0.12098,
+ -1.38950, -0.47301, -0.09634, -0.68567, -1.24055,
+ -0.18053, -0.21042, 0.05926, 0.98539, -0.51927,
+ 0.54184, 0.95370, -0.44613, 0.35295, 0.05765,
+ -0.44719, 0.78872, 1.72403, 0.07168, -0.81351,
+ -2.06002, -0.70296, -1.34491, -0.50843, 0.04395,
+ -1.46220, -0.70590, 0.37343, -0.33249, -0.29006,
+ 0.51288, -1.04725, -1.06966, 0.94720, -1.11772,
+ -1.19694, -0.63246, 0.38439, -0.16659, -1.01086,
+ 0.93367, 0.96960, 0.44271, 0.83306, 0.32252,
+ 0.15091, -1.41688, 0.80498, 0.73274, -0.74672,
+ 0.87679, 0.17201, -0.51406, -0.64294, 0.29530,
+ -0.87339, -0.68188, -0.58845, 0.31803, -0.02810,
+ -0.18284, -0.94473, 0.32943, 0.20469, -0.18078,
+ -0.34918, -0.38599, -0.53142, -1.71517, 1.55498,
+ 0.04529, -0.41210, -0.31658, -0.28591, 1.40182,
+ 0.44347, 0.12171, -0.00927, -0.26853, -0.45983,
+ -0.02174, 0.24924, -0.92399, -1.47916, 0.61874,
+ -0.21962, -0.87701, -0.24499, -0.31789, -2.91675,
+ 0.14481, -0.77955, -0.09180, -0.00317, -0.47476,
+ -0.84840, -0.51324, 0.03639, -0.03539, 0.14261,
+ -0.03639, 0.10127, 0.46480, 0.15325, 0.01055,
+ -1.31063, 0.26456, -0.69203, -0.66062, -0.11826,
+ 1.16524, 0.73562, -0.40157, 0.88238, 0.63043,
+ -0.01034, 0.25398, -0.74251, 0.05831, 0.43117,
+ -0.39506, 0.16914, 0.81523, -0.24976, -0.26056,
+ -1.66401, 0.02899, -1.89298, 0.09130, -0.56576,
+ -1.03235, 0.03758, -0.74710, -0.35810, 0.49252,
+ -0.33249, -0.26078, 0.60996, -0.96476, -0.44375,
+ 0.60165, -0.07322, -0.28690, 1.32222, 0.41510,
+ -0.13618, -1.58237, -2.05107, -0.57901, -0.00387,
+ 0.64954, 0.31708, -0.46925, -0.73803, -0.09523,
+ 0.96672, -0.33113, 0.25880, -0.18701, 0.27183,
+ -0.11779, -1.22934, -0.25881, 0.74385, 0.69666,
+ 0.37232, -0.09713, -0.50656, 0.01887, -0.90473,
+ -1.17386, -0.56362, -0.01845, -0.78814, -0.58474,
+ 0.00844, 0.39679, -1.51478, -0.36715, -0.21370,
+ -0.49409, -0.14386, -0.34275, -1.77429, 0.38840,
+ 0.34257, 0.50434, 0.11477, 0.55489, 0.06548,
+ 0.19802, -0.32000, 0.25839, -0.01401, 0.05650,
+ 0.28245, 0.51944, 0.94728, -0.12031, 1.15896,
+ 0.28441, -0.35558, -0.56990, 0.03018, -1.60632,
+ -1.43830, -0.00172, -0.16514, 0.42294, -0.41928,
+ -0.36765, -1.31621, -0.74179, -0.56972, -0.75711,
+ 0.90258, -0.33166, 0.75246, 0.27504, -0.13622,
+ -1.65513, 0.30815, -0.21901, 0.13782, 0.96477,
+ -0.36380, 0.56029, -0.50518, 0.04587, -0.08028,
+ 1.02113, -2.45920, -1.05953, -0.11171, -0.34403,
+ 0.26789, -0.74846, -0.76790, 1.28051, -0.04265,
+ 0.37655, 1.14539, 0.99457, 1.50095, -0.52289,
+ 0.29044, -0.34648, -0.44933, -0.74243, 0.51215,
+ -1.94392, 0.13655, -1.31833, -0.80017, -0.96082,
+ -0.88884, -0.08601, -0.24815, -1.09271, 0.54312,
+ -0.24946, -1.19258, -0.12443, 0.21164, -1.62581,
+ -0.08685, 0.18590, -0.67096, -0.05993, 1.16050,
+ 0.93780, 0.03243, -0.19104, -0.73482, 0.46122,
+ 0.50559, -2.26677, -0.01241, 0.58872, -2.13803,
+ -0.94799, -0.76818, -1.05059, 0.78527, -0.43918,
+ -0.49501, -1.15370, -0.37426, -1.42503, 0.25037,
+ 0.88382, 0.09625, 0.22353, 1.32863, 1.71000,
+ -0.47232, 0.84886, -0.45620, 0.41299, -0.10000,
+ -1.01746, -0.34363, -0.26025, 0.07697, -1.27381,
+ -0.25941, -0.84029, -0.59905, 0.29271, -0.30282,
+ -0.28216, -0.18050, -0.42832, -0.44229, 0.79449,
+ -0.11801, -0.25464, 0.53369, 0.21996, 1.17499,
+ 0.22904, -0.95998, 0.42900, -0.15633, 0.15253,
+ -1.17588, 0.03479, -0.52487, 0.72958, 0.71571,
+ -0.06515, 0.00162, -0.59103, -0.99382, 0.11005,
+ -0.29956, 0.62816, -1.40934, 0.21110, -0.57670,
+ 0.27664, -0.01728, 0.96908, 0.71180, 0.38084,
+ -1.13189, 0.39319, 0.11676, -0.58078, 0.30540,
+ -0.71733, 0.10551, 0.10059, 0.90708, -0.13329,
+ -0.47664, 0.04405, -0.35863, -1.38725, -1.29261,
+ -1.30848, 0.31963, -0.04782, -0.18195, 0.77565,
+ -0.34312, 0.58478, -0.13980, 0.53244, -0.69704,
+ 0.03976, 0.02290, 0.02656, -0.13177, -0.75530,
+ -0.01724, -0.38432, -0.29525, 0.76212, -0.61117,
+ -0.99057, -0.82627, 0.11837, -0.56951, -1.55074,
+ -0.11150, 0.68401, 1.06838, -1.08682, 0.41065,
+ 0.31257, -0.78748, -0.51040, -0.86278, 0.03890,
+ 0.16274, -2.37877, 0.16119, 0.53832, 0.80299,
+ -0.44318, 0.51756, 0.14716, 0.39734, -0.59091,
+ -0.87638, 0.51240, -0.10130, -0.63007, -1.28249,
+ -0.77009, -1.00929, -1.69958, -0.89430, 0.62496,
+ 1.16018, 0.56723, -0.52142, -0.16592, -0.45892,
+ -0.73957, -0.32757, 0.51289, 0.35968, 0.48686,
+ 0.57193, -0.75315, 0.00362, -0.32782, -0.34566,
+ -0.47906, 0.43787, -0.14964, -0.80799, -1.15644,
+ -0.51636, 0.14932, 0.29630, -0.79507, 0.14620,
+ 0.05168, -0.55423, -0.63607, -0.45526, 0.73782,
+ 0.37454, 0.69863, -0.03113, -1.75045, 0.33300,
+ 0.02508, -0.69499, 0.04733, -0.23627, -0.37103,
+ -1.10413, -0.22378, -0.56322, 0.52200, -0.03253,
+ 0.04360, 0.22934, 0.38141, -0.29349, 0.22647,
+ 0.28772, -0.30133, 0.22556, -0.00325, -2.09585,
+ 0.82184, -0.20846, 1.20822, -1.01748, 0.43575,
+ -0.32811, -0.15358, 0.09847, -0.88580, 0.07717,
+ 0.08516, -0.43556, -0.48276, -0.40685, 0.29081,
+ -0.56271, -0.45637, 0.81685, -0.47836, -3.28118,
+ 1.72635, -1.75352, -1.60328, -1.41781, 1.33224,
+ 1.49973, -1.27198, -1.80074, -2.52646, 0.96703,
+ 1.60879, -1.46153, -1.81106, -1.49761, -1.91313,
+ 1.69681, 1.72337, -1.70555, -1.98991, 1.78116,
+ -1.69085, 2.35355, 1.41601, 1.32029, 1.56978,
+ 1.69020, 1.29577, -1.64406, 1.22962, 1.74042,
+ 0.12119, -1.72634, 1.75352, 1.60328, 1.41781,
+ -1.33223, -1.49972, 1.27196, 1.80074, 2.52645,
+ -0.96704, -1.60879, 1.46154, 1.81107, 1.49761,
+ 1.91313, -1.69680, -1.72337, 1.70556, 1.98991,
+ -1.78116, 1.69084, -2.35356, -1.41601, -1.32029,
+ -1.56977, -1.69019, -1.29576, 1.64407, -1.22962,
+ -1.74042, -0.12120,
+};
+
+float const r19_3[(na*19+1)*30+(30+1)*2] = {
+ 0.03220, 0.47480, -1.91590, 0.03789, -1.02207,
+ -0.27466, -0.34365, -0.60255, 0.93793, -0.09442,
+ -0.33837, -0.00542, 0.35547, -0.57896, 0.94074,
+ 0.09032, -0.68986, 0.46323, -0.19205, -0.13742,
+ -0.41033, -1.15934, -1.11347, 0.87720, 0.78365,
+ -1.21580, -0.47716, -0.81291, 1.17809, -1.37266,
+ 1.48248, 0.78770, 0.12449, 0.03965, -0.19367,
+ 0.39082, -0.42996, 0.34177, -1.07950, -0.35514,
+ -0.92504, 0.05562, 0.66199, -0.03887, -1.00105,
+ 0.43184, -1.01208, -0.12050, 0.16238, -0.19500,
+ 1.13992, -0.47994, 0.45301, 0.18971, -0.05063,
+ -0.78611, 0.10944, -0.36299, -0.49391, -0.17085,
+ -0.44283, -1.24991, 0.18318, 1.20109, -0.76455,
+ -0.08772, 0.93688, -1.47485, -0.42781, -0.80959,
+ 0.24358, -0.76190, -0.57483, -0.65232, -1.21698,
+ 0.50536, -0.48025, 0.57490, 0.71729, 0.30585,
+ -0.89241, -0.09084, 1.24718, -0.57124, 0.06588,
+ -0.03571, -0.18892, -0.97361, 0.51472, -1.87385,
+ -0.39194, 0.11306, 1.14220, -0.50946, 1.80904,
+ -0.25847, 0.40967, -1.02573, 0.92060, -1.14374,
+ -0.50692, -1.01080, 0.03161, 0.04640, -0.20717,
+ 0.22006, -0.22769, 0.16819, 0.33053, -0.16990,
+ 0.27380, 0.38527, -0.07936, 1.00027, -0.76343,
+ -0.51905, -0.40981, -0.18906, -0.48690, -0.73020,
+ -0.86904, -0.82811, -0.38695, -0.00389, -0.26591,
+ 0.27801, -0.11891, -0.53942, -0.51052, -0.17698,
+ -0.51619, -0.72386, -1.87792, 1.56194, 0.54777,
+ -0.00540, -0.46551, 0.24038, 0.17821, -0.08745,
+ -0.14442, -0.19510, -0.54025, -0.94931, -0.12250,
+ 0.58970, 0.38265, -1.35091, -1.27371, 0.38579,
+ -1.16601, 0.24629, -0.34184, 0.12745, 0.13177,
+ -0.44365, 0.17437, 0.61199, 0.90153, -0.92170,
+ -1.08347, 0.37621, -0.71664, 0.13577, -0.67791,
+ 0.32418, 0.58792, 0.49937, -0.24002, -1.36135,
+ 0.14212, -0.64889, -1.62508, -2.42147, 0.62486,
+ 0.99589, -0.03799, -1.42627, 0.01565, 0.81739,
+ -0.33946, -0.53684, 0.10002, 0.28940, -0.04663,
+ -0.47519, 0.96970, 0.48074, 1.05016, -1.30912,
+ -0.37130, 0.13712, -0.41461, 0.19242, -0.13273,
+ -0.72806, -0.36972, -0.83097, 0.25026, -1.48981,
+ -0.66442, -1.05330, -0.32475, 0.13170, 1.00829,
+ 1.55895, -0.15522, 0.06868, 0.92348, -0.10000,
+ 2.17074, 0.29518, 0.32249, -0.35749, -1.16031,
+ 0.56272, 0.95121, 0.06224, -0.34167, -0.97726,
+ 0.06221, -1.41572, 0.01153, -1.29922, 0.33986,
+ 0.35324, -1.34877, 0.16303, -0.34794, -1.71199,
+ 0.79277, 0.36582, 0.55339, 0.35273, -0.40540,
+ 0.59448, 0.29925, 0.58995, -0.32856, 0.40707,
+ -1.28022, -0.99237, 0.20048, -0.38023, -0.40656,
+ -0.26761, -0.50418, -0.08509, -1.87898, 0.01257,
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+ 1.55606, -1.31925, -1.77485, -1.79740, -1.56556,
+ 1.87896, 1.25269, -1.63457, -1.72965, 1.58500,
+ -1.48411, 1.58084, 1.69072, 1.56002, 1.28039,
+ 1.85392, 1.93610, -1.53595, 1.29631, 1.60084,
+ 0.15991, -1.60903, 1.85541, 1.65536, 2.20416,
+ -1.52600, -1.24650, 1.57588, 1.87321, 1.43852,
+ -1.00239, -1.55605, 1.31925, 1.77485, 1.79741,
+ 1.56557, -1.87895, -1.25269, 1.63458, 1.72965,
+ -1.58499, 1.48411, -1.58084, -1.69071, -1.56002,
+ -1.28039, -1.85393, -1.93611, 1.53596, -1.29632,
+ -1.60084, -0.15992,
+};
+
+float const r19_4[(na*19+1)*30+(30+1)*2] = {
+ -0.52512, -0.57061, -0.47833, 0.74562, 0.13606,
+ -1.22673, 0.50148, -0.75317, 0.80071, -0.31284,
+ -0.47380, 0.30504, 0.04312, 0.55731, -1.02401,
+ 0.21646, -0.42040, -0.01278, -0.51610, 0.15129,
+ -0.10968, -1.21615, -1.19156, 0.16322, 0.20324,
+ -0.45509, -0.11012, -1.12806, -0.69610, 0.40497,
+ 0.57874, 0.09826, 1.17079, 0.49638, 0.30918,
+ -0.63867, -0.99929, -1.00298, 0.52345, -0.23504,
+ -0.54067, 1.49902, -0.06635, 0.97514, 0.07084,
+ -0.61052, 1.18170, -0.26343, -0.28125, 0.96778,
+ -0.42122, 0.15224, 0.68115, 0.59041, -0.13359,
+ -1.91787, -0.63670, -0.58787, -1.57480, -0.25123,
+ 0.02335, -0.41276, -0.25149, -0.17390, -0.46021,
+ -0.35404, -0.74555, -1.05606, 0.88234, 0.44768,
+ -0.09685, -0.39392, 0.44847, 0.13600, -0.73519,
+ -0.23450, 0.11655, -0.25346, 0.30343, -0.48803,
+ 0.49600, 0.42724, -0.03124, -1.00120, -0.25858,
+ -0.34703, -0.34008, -1.06331, 0.98746, 0.59246,
+ -1.28711, -0.56317, 1.60093, -0.40671, -0.27514,
+ 0.26474, 0.05156, -1.05657, -0.29564, -0.05862,
+ 0.03406, -0.13348, -0.57252, 0.47992, -0.11958,
+ 0.98075, 0.13013, 0.41034, -1.66434, -0.36988,
+ 0.32582, -0.63250, 1.28645, -0.03932, -0.42189,
+ 0.65225, -0.78492, 0.52287, -1.09198, -0.14881,
+ -0.52577, -0.66364, -0.79064, -1.04888, 0.70694,
+ 0.20052, 0.00241, 1.02120, -0.80931, 0.31756,
+ -0.04491, -0.32826, -1.54657, 0.42862, 0.46821,
+ -0.32451, -1.81184, -1.52955, -0.84642, 1.10387,
+ -0.30025, -1.04549, 0.43742, -0.31207, 0.56012,
+ 0.87602, 0.51730, -0.62610, 0.22098, -1.80043,
+ -1.62253, 0.39284, 0.55880, -0.30842, 1.00431,
+ 0.29397, 0.75936, -0.67490, -0.45847, -0.55609,
+ -0.10372, -1.80961, -0.05556, -0.01347, 0.54464,
+ -0.31600, 0.43567, 0.96831, -0.53071, 0.19937,
+ -0.84313, -0.62365, 0.34178, -0.13354, 0.28595,
+ -0.20683, 0.52793, -0.62588, -0.50134, -0.12839,
+ 0.46455, -0.19851, -0.13882, 0.04356, -1.78520,
+ -1.16300, 0.13993, 0.44937, 1.06006, -0.80419,
+ 0.05753, 0.88169, -0.78021, -0.02632, -1.34804,
+ -0.49620, -0.67452, -0.77814, -0.16853, -1.32341,
+ -0.18435, -0.21342, -0.03342, 0.29050, -0.15619,
+ 0.42807, 1.03996, 0.57582, 0.44687, -0.10000,
+ 0.62442, -0.56939, -1.17213, -1.24023, -0.64541,
+ -0.34381, 0.52275, -0.24802, 0.68615, -0.65044,
+ 0.00106, 0.60767, -0.81998, -0.44062, 0.07774,
+ 1.10588, -1.02450, 1.00687, 0.00674, -1.21425,
+ 1.16304, 0.11799, -1.71423, 0.54148, -0.54214,
+ 0.91879, -0.09518, -1.89890, -0.72546, 1.06223,
+ -1.69002, -1.02037, 1.36582, 0.04454, 0.03615,
+ -0.31698, -0.30333, 0.27798, -0.38997, 0.53156,
+ 0.41062, 0.82294, -0.27785, -0.09106, 0.02737,
+ -0.63934, 0.06683, -0.55999, -1.26025, 0.17614,
+ -1.62978, 0.63033, 0.29478, -1.32999, 0.94729,
+ -1.12347, 0.94479, 0.52853, -0.56084, 0.40071,
+ 0.36935, -0.14585, 0.46584, 0.17750, 0.63765,
+ -0.90876, 0.23294, 0.77552, 0.71460, -0.14525,
+ 0.76567, -0.34651, 1.50757, 0.44127, -0.33308,
+ -0.13751, -0.67407, -1.61451, 1.10155, -0.70535,
+ -1.93487, -1.20143, -1.01609, 0.09663, -0.54345,
+ -0.81368, 0.10867, -0.65331, 0.22430, -1.06490,
+ 1.16647, -0.11202, -0.49836, 0.10185, -0.46408,
+ 0.18609, 0.56082, 0.74258, 1.14246, -1.29433,
+ -0.97926, 0.20965, 0.64868, -0.50482, -1.12977,
+ 0.08929, -0.63309, -0.40828, -0.80872, -0.12787,
+ -0.89147, -0.80777, 0.39497, -0.14377, -0.71008,
+ -0.10491, 0.76880, 0.40729, -0.02438, 1.19848,
+ 0.46156, -0.08116, -0.66661, -0.56530, 0.11141,
+ -0.22478, -0.36388, -0.41277, 1.25017, -1.37372,
+ -1.48244, 0.59518, 1.59965, -0.59339, 0.07618,
+ -1.69183, -0.13016, 0.29033, -0.83516, -0.01496,
+ 0.56574, 0.08198, 0.83857, -1.50693, 0.66542,
+ -0.12051, -0.00390, -1.07455, 0.63264, -0.40035,
+ -0.00027, 0.38464, -0.61119, -0.81772, 1.10270,
+ 0.79681, 0.25868, -0.05081, -0.57272, -1.54711,
+ -0.24666, 0.38929, -0.32145, -0.76173, -0.70706,
+ 0.51182, -0.11341, 0.58204, 0.52875, -0.01815,
+ 0.51000, 0.80058, 0.04690, 0.43441, -1.32738,
+ -0.71903, -1.08197, 0.52726, 0.28218, 1.21289,
+ -0.72259, -1.37064, -1.04473, -0.05271, -0.70192,
+ 0.15772, 0.57638, -0.43990, 0.03548, -2.76677,
+ -0.33265, -0.27816, -0.75166, 0.26521, 0.48793,
+ -0.32216, -1.56732, 0.14617, -0.17456, -0.21569,
+ 0.85402, 0.48790, -0.83624, -0.24383, 0.28697,
+ 0.44388, 0.05170, -0.00616, 0.64379, -0.05268,
+ -1.45110, -0.55092, -0.48138, 0.37252, 2.46658,
+ -0.35752, 0.44969, 0.82319, 0.33857, -1.32440,
+ -0.46501, -0.80916, -0.21010, 0.01181, 0.06500,
+ -0.64560, -0.71505, -0.79173, 1.39426, -0.49929,
+ -0.80233, -1.43378, -0.68902, -0.55169, 0.50222,
+ 0.48202, 0.64911, 0.21973, 0.11124, 0.22443,
+ -0.59883, 0.10220, -0.99171, -0.16209, -0.47198,
+ -0.01923, 0.00300, -0.25134, 0.35742, -0.66683,
+ 0.13180, 0.25827, -0.00328, -0.38314, -0.41256,
+ 0.47684, 0.87587, -1.17322, 0.00348, -0.56540,
+ -1.48824, 0.08789, 0.37706, 0.22328, -0.64535,
+ -0.53303, -0.38467, -0.91801, 0.48216, -0.01640,
+ -2.02839, 0.64949, 0.30952, 1.89819, 0.29671,
+ 0.42669, -0.07693, -0.53102, -0.18162, 0.11218,
+ 0.39103, 0.46467, 0.35150, -0.15935, 0.53903,
+ -1.11102, -0.29449, -0.14626, -0.84927, 0.16550,
+ -1.22704, -0.12414, -1.16983, -0.02179, 0.98087,
+ -0.01481, 0.61631, 0.47433, 0.45942, 0.36460,
+ 0.39911, 0.15905, -0.32797, 1.62264, 0.51644,
+ 0.27640, -1.15591, -1.47016, -0.56090, -1.34095,
+ 0.02799, -0.15227, -2.39995, -0.84820, -0.65112,
+ 1.24136, 0.57742, -0.41485, -0.10973, -2.00444,
+ -0.10675, 0.27580, 0.69740, 0.26248, 1.12783,
+ -0.57125, 0.07106, -0.44041, -0.03494, 0.43583,
+ -0.87887, 0.31677, -0.84530, -0.47082, -0.40697,
+ 0.25458, -0.09942, -0.95503, 1.32988, 0.11552,
+ -0.52323, 1.01759, -0.24827, -0.49194, -1.29143,
+ -0.95727, 0.24777, 0.89972, 1.18299, 0.44126,
+ -0.46131, -1.10222, 0.69027, 0.40129, -0.48202,
+ -0.37873, -0.95247, -0.64702, 0.06397, 2.77328,
+ 0.66799, 0.54475, 0.76417, 3.17615, 2.21212,
+ -0.16951, 1.05078, 0.08369, 0.33078, -2.34267,
+ -1.01971, 0.75932, -2.46883, -3.08817, -1.20471,
+ -0.90492, -1.82981, -0.55744, -1.00580, 0.68466,
+ 0.86170, 0.70891, 0.57384, 1.48788, 1.00203,
+ -0.03270, -0.32439, 0.24895, 0.45362, -0.75975,
+ -1.16095, -0.47618, -0.22703, -2.44750, -2.00230,
+ 0.04416, 0.54199, 0.14202, -1.18353, 0.10000,
+ 0.68160, 0.40279, 1.17159, 0.39946, 1.44678,
+ 0.72941, -1.25314, 0.00648, 0.54209, 0.80300,
+ -0.25218, -0.62599, -0.60300, -1.48960, -2.27233,
+ 0.05108, -0.96391, -0.75249, -1.00559, 0.90086,
+ -0.48162, 0.06812, -0.69919, 0.74236, 0.69660,
+ 1.37732, 0.26090, 0.49028, 0.37432, -1.04996,
+ -0.24774, -0.30212, -0.13523, -0.37859, -0.47245,
+ -1.31788, -1.63013, -0.47173, 0.24973, -0.45846,
+ 0.72076, 0.01850, 0.35861, 1.97210, 1.87641,
+ 0.40134, 0.30921, 0.88762, -0.46920, -0.88199,
+ 0.76082, 0.64598, -0.75952, -1.55364, -0.23636,
+ -0.32665, -0.57097, -1.44223, -0.96209, -1.12036,
+ -0.70092, -0.81463, -0.93806, -0.23168, -0.19916,
+ 0.56825, 0.73853, 0.03476, -0.32437, 0.39776,
+ 0.01468, 0.85355, 0.37438, -1.15158, -0.54163,
+ 1.49308, 0.10191, -0.20299, -0.07009, -0.93307,
+ -0.73938, -0.44919, -0.58982, -1.70850, -0.65468,
+ -0.80374, -0.15434, -1.07995, 1.20144, -0.08229,
+ -1.11121, 0.36480, -1.30859, -0.14877, -0.85356,
+ -0.62739, -0.54931, 0.35984, 0.41384, 0.55017,
+ -0.08064, 1.41675, -1.04110, 0.61251, 0.21165,
+ -1.11765, 0.23229, 0.03180, 0.86197, 1.13241,
+ 0.44031, -0.34713, -0.48410, 0.57586, 0.72879,
+ -0.48847, -0.31734, 0.28553, 0.57649, -0.02304,
+ 0.05895, -1.88009, -0.89341, -1.51578, -1.77613,
+ 0.35420, 0.39902, -0.42359, -0.02543, -0.53762,
+ -0.61049, 1.23788, -0.66221, 0.47107, -1.90044,
+ 0.57832, -1.41253, -0.56776, -0.06781, 0.15264,
+ -0.72116, -0.67442, 0.43162, 0.14529, 0.22423,
+ 0.28674, 0.11211, 0.01877, -0.06387, -1.23333,
+ 0.46370, 0.17427, -0.01160, -0.09784, 0.49036,
+ 1.42846, -0.81777, 0.18963, -0.12474, -0.18342,
+ -0.05991, -1.15045, -0.17867, -0.81772, -0.26315,
+ -0.23989, -0.93266, 0.04521, 0.36890, -0.50331,
+ -0.86320, -0.47762, -0.05682, 0.10668, -0.72901,
+ -1.02335, 0.00666, 0.51785, 0.15535, -0.37478,
+ 0.86568, -0.33878, -1.88215, 0.30565, -0.69464,
+ -0.19624, 1.12528, 0.66203, 0.26118, -2.56458,
+ 0.50516, -0.03914, -0.08241, 0.71158, 0.16868,
+ 0.53074, -0.29872, 0.96896, 1.05767, 0.44174,
+ -0.45896, -0.92056, -0.20548, -0.64427, -1.41323,
+ -0.55239, -0.29163, -0.66348, -0.22318, -0.04774,
+ -0.95841, -0.19652, -0.97459, -0.65593, 0.71231,
+ -0.48517, -0.21312, -1.34071, 0.89391, -1.40123,
+ 1.30955, -1.01827, 0.26215, 0.29640, -0.11227,
+ -1.54127, -0.33140, 0.23080, 0.27891, 0.23423,
+ 0.64445, 0.79272, -0.41879, -0.11324, -0.47191,
+ -0.58261, 1.22860, 0.59131, -0.69813, -0.02919,
+ 0.01321, -0.02419, -0.57529, 0.02795, 0.13016,
+ -0.31568, -0.98421, -1.03136, -0.22367, -0.03633,
+ -0.19524, 1.08691, -0.59337, 0.98735, 1.16832,
+ 0.61865, -0.07302, 2.09429, 2.17082, 0.10665,
+ -0.99247, 0.92881, 0.92382, -0.23825, -1.39114,
+ -0.40754, -1.62209, -1.72574, -1.72904, -1.27931,
+ -0.57888, -1.38212, -0.23785, 0.04366, 0.98035,
+ 0.46811, -0.13739, -0.05266, 0.22788, 1.03736,
+ -0.78102, -0.30675, -0.35506, 1.15107, -0.87624,
+ -1.30117, 0.66337, -0.31024, -2.72895, -0.59597,
+ 0.09803, -0.70651, -0.34461, 0.19512, 0.26033,
+ -2.12851, -0.94791, -0.85829, -1.12292, -0.47080,
+ -0.53192, -0.90282, -0.47526, -0.96818, 0.71783,
+ 0.09569, 0.77114, 1.26835, 0.21840, -2.02171,
+ 0.85794, 1.24882, 1.05766, 0.10539, 1.76990,
+ -0.49792, 0.21148, 1.27013, 0.18186, 1.37822,
+ 0.37286, 1.41121, 0.51089, -0.15608, -0.35632,
+ 0.91590, -1.61574, -0.50798, 0.39547, -0.33601,
+ -3.22446, -2.33436, -0.58369, 1.14306, -1.40355,
+ 0.67038, -0.35794, 0.98663, 1.78243, -0.06633,
+ 1.00486, 1.15175, 1.87862, -0.24342, -0.11733,
+ 0.56693, 0.78959, -1.10249, -1.18629, 0.53645,
+ -0.96329, -3.55714, -1.15795, -0.50517, -0.31166,
+ -0.69848, -0.77027, -1.03221, -0.63735, -1.45015,
+ -0.94563, -1.55731, -0.08662, -0.87612, -1.65680,
+ -0.74621, -1.00757, 2.28175, -0.95404, 0.54040,
+ 1.08004, -0.74133, -1.73167, 1.00721, 1.92412,
+ 1.20789, 0.65787, 1.43716, -0.36068, -1.32458,
+ -2.65356, -1.16692, -0.40042, 0.38485, -0.38055,
+ -1.31338, 0.15926, -1.11933, 0.73394, -1.18694,
+ 0.35874, 1.29998, -0.93935, -0.31198, 0.76049,
+ 1.06923, 1.01424, 0.31231, 1.78905, -0.10000,
+ 0.26268, 0.83411, -0.04866, 1.03764, 1.26339,
+ 1.17505, 0.89379, -0.50680, 0.97856, -0.09022,
+ -1.54859, -0.93550, -0.61895, -0.64913, 0.10553,
+ -0.54331, -0.87254, -1.17254, -0.77538, -0.32417,
+ -1.47992, 0.93255, 0.14166, 0.22165, -0.42313,
+ 0.47380, 0.12860, 0.50075, -0.83829, 0.31250,
+ -0.14530, -0.86984, 0.40977, -0.53983, 0.00932,
+ -1.50192, -0.13281, 0.02278, -0.74433, 0.13912,
+ -0.74519, -0.36693, -1.55015, -0.44424, -1.60973,
+ -1.21988, -0.48406, -1.00432, -1.22035, -0.03819,
+ -1.62307, 0.34597, -0.14787, 0.48233, 0.36084,
+ -0.47550, 0.01431, 1.62992, 1.52196, 0.68163,
+ 0.32683, 0.54626, 0.69231, -1.14391, 0.03968,
+ -0.86449, -0.11870, 0.56483, 0.13127, 0.72940,
+ -0.12452, -0.02255, -0.08315, -0.78358, -0.23505,
+ 0.61417, 0.41264, -0.57200, -0.54295, 0.15599,
+ 0.25214, -0.67038, -0.09855, -0.85537, 0.17370,
+ 0.37481, -0.18095, 0.94948, 1.35080, 0.47507,
+ 1.02293, -0.65471, 0.09067, -0.03769, -0.78297,
+ -1.01826, -0.20852, -0.06898, -0.43261, -0.92578,
+ -0.82714, 0.06055, -0.00863, -0.53415, -1.43276,
+ 0.11233, -0.68826, -1.26151, 0.53834, -0.36993,
+ -0.15927, -1.03701, 0.43067, -0.12343, 0.41258,
+ -1.07954, 0.46541, 0.34357, -0.09371, 0.22543,
+ 0.13884, 0.05841, -0.88589, -0.03717, -0.69972,
+ 0.49481, -0.21859, -0.69429, -1.53120, -1.37331,
+ -0.73753, 0.21967, 0.26243, 0.17167, -1.05164,
+ 0.30221, -0.82940, -0.70909, 0.52490, -0.74495,
+ 0.48316, 0.39909, 0.81005, 0.08013, 0.30116,
+ 0.05030, 1.27009, 0.10734, -0.00074, -0.32828,
+ -0.75467, 0.66644, 0.71975, 1.84371, -0.30397,
+ 0.38520, -0.32666, -0.23165, -0.56126, -0.23301,
+ -0.05782, -0.53217, -0.24033, -0.99139, -0.01742,
+ -0.29065, -0.34686, -1.12069, 0.81526, -0.04678,
+ -0.17700, 0.44664, -0.22916, -0.14245, -0.25035,
+ -0.53695, 0.73770, -0.03567, -1.06207, -0.40881,
+ -0.51814, -0.25680, -0.52974, -0.26084, -0.54745,
+ -0.15565, -0.13941, -0.05998, -0.25741, -3.01450,
+ 0.29014, -0.46581, 0.18171, 0.06046, -0.70466,
+ -0.70387, -0.27240, 0.51637, -0.59508, -0.07925,
+ 0.36731, 1.77256, 0.06188, -0.45290, -0.33152,
+ -0.90466, -0.76875, -0.36388, -0.47810, 0.38510,
+ -0.30292, 0.63770, -0.07198, -2.25267, -0.51629,
+ 0.29602, -1.65411, 0.76281, -1.93130, -0.81829,
+ 0.38219, -0.01734, 0.38627, -0.23340, 0.76101,
+ 0.20568, 0.95343, 0.13445, -0.59524, -0.71990,
+ 0.80736, 0.49538, 0.57017, 0.46486, -1.15116,
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+ 0.84230, 0.45607, 0.26962, -0.37181, -0.63988,
+ 0.17320, 1.69803, -1.12365, 1.15284, -0.37761,
+ -0.13464, -0.10532, 0.42918, -0.16809, -0.55601,
+ -1.00423, -2.11164, -1.14849, -0.20183, -0.21491,
+ -0.06716, -1.29830, -0.36985, 0.14574, 0.83893,
+ -0.07079, 0.40419, -1.16563, -0.28570, 0.63328,
+ -1.09908, -0.44441, 0.02441, -0.07760, 0.67294,
+ 0.82941, -1.56461, -0.67414, 0.86537, -0.84834,
+ 0.61377, -0.13353, 1.17594, 0.12746, 1.44639,
+ 0.44462, -0.85686, 1.24226, 1.62406, -0.38373,
+ 0.48347, -1.47452, 0.55536, -0.47998, -0.78745,
+ -0.96587, -0.00713, -1.09257, -1.12454, -1.33685,
+ 0.10459, -0.79229, -0.10631, -1.05379, -0.65247,
+ 0.29171, 0.92871, -0.02474, -0.24369, 0.18929,
+ -1.14542, -0.74875, -1.11374, -1.09572, 1.10282,
+ -0.13466, -1.18435, 1.52182, -0.22847, 0.96880,
+ 0.12868, -0.82723, -0.47954, 0.79683, -2.21688,
+ -0.99301, -0.69567, -1.33443, -0.20209, -0.28010,
+ 0.12727, -0.76205, -0.75549, 0.07612, -2.13357,
+ 0.49155, -0.49718, 1.04849, 1.53474, 0.72302,
+ 1.15115, 0.72399, 0.07486, 1.41529, -0.10000,
+ 0.18307, 1.29510, -0.53958, -1.52941, -0.62407,
+ 0.79027, -0.04534, -0.46798, -0.25715, -0.85873,
+ 0.67952, -0.08334, 0.00498, 0.07334, -0.85601,
+ -0.09292, -0.76485, 0.10695, 0.37139, -0.41662,
+ 0.42746, -2.81111, -0.17319, 0.49579, 0.98770,
+ 0.29757, 0.10594, 1.56006, -0.28814, -0.24928,
+ -0.32183, -0.66468, -0.00824, -0.43154, 0.48338,
+ 1.12242, 0.63260, -0.66762, -1.11105, -0.36368,
+ -0.02301, -1.37594, -0.12138, 1.81744, -0.17294,
+ -0.84167, 0.07598, 0.50972, -0.09527, 0.12516,
+ 0.04783, -0.23292, 0.08712, 0.28900, -0.91641,
+ -0.11008, 0.78514, -0.01795, -2.52787, -0.07396,
+ -0.19283, -0.41699, -0.42102, 0.29336, 1.06015,
+ 0.09736, -0.27044, 0.43175, -0.89939, 2.19764,
+ -0.27010, -0.75783, -1.16585, 0.11682, -0.07174,
+ -1.46122, -0.71024, 0.36309, -0.07547, -0.72854,
+ -1.15006, 0.89926, 0.07991, -0.38246, -2.02902,
+ -1.48269, -0.20343, -0.05823, -1.28783, 0.41341,
+ 0.63228, -0.01460, -1.94470, -0.30408, -0.36230,
+ 0.65383, -0.81865, 0.83966, 0.53999, 0.07298,
+ 1.02985, -0.37484, 0.86236, 0.55312, 0.87895,
+ -0.85321, 0.34722, -0.68096, 0.76309, -0.42494,
+ 0.09427, -0.58921, -0.66001, -0.82390, 0.91990,
+ 0.02239, -0.21457, -1.09706, -0.25705, -0.70510,
+ 0.08344, -0.57154, 0.00535, 0.37848, 0.22639,
+ 0.03319, -0.80490, 0.45524, -1.17759, 0.37955,
+ -0.18216, 0.59123, 0.26225, -1.97854, -0.03972,
+ -0.51810, 0.20678, -0.97152, 0.34851, 0.30839,
+ -0.46482, 0.40544, -0.23065, 0.69201, 0.24415,
+ -0.67928, -0.25020, -0.74177, -1.87198, 0.20259,
+ 0.46648, 0.08200, -0.76463, -0.61803, -0.49452,
+ -0.13978, -0.38292, -0.99757, 0.13097, 0.46532,
+ 0.50436, 0.76534, 0.14743, 0.98612, 1.01646,
+ 0.29260, -0.66371, -0.98864, -0.33878, -0.88976,
+ -0.82778, -1.13485, 0.99051, -0.27072, -0.29993,
+ -0.97104, -1.07769, -0.20968, 0.10177, 0.48574,
+ -0.04325, -1.21969, 0.32926, 0.64017, -0.01939,
+ 0.22495, -0.22595, 0.50385, 1.24840, -2.60407,
+ 1.53792, -1.31412, -1.50673, -1.71333, 1.43954,
+ 1.85377, -1.44652, 1.47599, -1.68391, 0.97621,
+ 1.87350, -1.52706, -1.59808, -1.54666, -2.66210,
+ 1.40955, 1.81621, -1.65154, -2.07174, 1.62269,
+ -1.28605, 1.58604, 1.40303, 1.72626, 1.89107,
+ 1.35868, 1.61129, -1.38984, 0.94217, 1.30023,
+ -0.10548, -1.53792, 1.31411, 1.50672, 1.71333,
+ -1.43955, -1.85377, 1.44652, -1.47599, 1.68391,
+ -0.97620, -1.87349, 1.52706, 1.59808, 1.54667,
+ 2.66210, -1.40955, -1.81620, 1.65155, 2.07175,
+ -1.62269, 1.28605, -1.58604, -1.40303, -1.72626,
+ -1.89106, -1.35868, -1.61129, 1.38985, -0.94217,
+ -1.30024, 0.10547,
+};
+
+float const r19_5[(na*19+1)*30+(30+1)*2] = {
+ 0.27987, -1.93430, -1.41800, -0.24643, -1.49231,
+ -0.47784, 1.09420, -0.48696, -0.65600, 0.19047,
+ 0.12281, -0.82516, 0.20635, 0.82342, 0.37617,
+ -0.10692, -0.11367, -1.74304, 1.26575, 0.85535,
+ 0.88337, 0.81226, -0.86114, -1.60720, 0.50937,
+ -1.20673, -0.12290, -0.32637, 0.79542, -0.12390,
+ 0.07122, -0.10421, 1.07985, -0.22284, -0.14770,
+ -0.25688, -0.94948, -0.78272, 0.57044, 0.03971,
+ -0.88782, 0.51873, -0.30938, 0.55343, -0.12755,
+ -0.68925, 0.04319, -0.74687, 0.06047, 1.54328,
+ 1.09718, 0.68823, 0.08584, 1.24789, -0.69850,
+ -2.00331, -0.39664, -2.16726, -0.58629, 0.03422,
+ 0.52918, -0.30834, -1.05237, 0.16096, -1.60515,
+ -0.62069, 0.53268, -1.14077, 0.13916, -0.31752,
+ -0.23490, -1.24769, 0.18706, 0.49039, -0.52505,
+ -0.08728, 0.06793, 1.07883, -0.03866, 0.25067,
+ 0.12079, 0.83865, -0.53907, -0.71322, -0.58594,
+ -0.70735, -0.70460, -1.03944, 1.34215, -0.54647,
+ 0.95280, -0.96589, -0.17272, -1.43659, 0.57329,
+ 0.18455, 0.23936, 1.04237, -0.86219, -1.23041,
+ 0.65235, -1.03770, 0.96100, 0.51902, -0.38049,
+ 0.79958, -0.29520, -0.55420, -0.56734, -0.35343,
+ -0.37735, 0.61514, 0.36123, -0.07965, -0.37629,
+ 0.51742, -0.12650, 0.24036, 0.46116, -0.01237,
+ -0.65802, -1.08089, 1.24181, -2.10588, -1.24261,
+ 0.19019, -0.31891, -0.24052, -0.85703, -0.16463,
+ 0.43533, -0.17229, 0.85990, 0.32466, -0.44053,
+ -0.15577, -0.32049, -0.05652, -1.11014, 0.42823,
+ -0.18404, -1.16828, -0.26311, -0.57132, -0.02545,
+ 0.54741, -0.14933, -0.35986, -0.51856, -0.53650,
+ 0.30972, -0.89876, 0.45378, 0.15188, -0.45737,
+ 0.70893, 0.27109, 0.43349, -1.99394, -1.01799,
+ -1.44021, 0.08350, -1.09557, -0.30349, 0.39975,
+ 0.97186, 0.06752, 1.16780, -0.21572, -1.20383,
+ -0.51759, -0.34165, 0.97320, -2.01329, -0.11588,
+ 0.76465, 0.33931, -0.60882, -0.58683, 0.41415,
+ 0.30189, -0.48969, 0.95000, -0.53580, -0.99612,
+ -0.89935, -0.35942, 0.49464, 0.84319, -0.02352,
+ -1.73768, -0.37894, -0.61492, -1.08414, 0.58178,
+ -0.87539, 0.06891, -0.29233, -0.74413, -1.94635,
+ -1.08664, -0.05664, -0.13511, 0.93461, 1.21902,
+ 1.26156, 0.56333, 0.52482, 0.11886, -0.10000,
+ 0.09553, 0.66660, -2.09688, 0.77240, -0.44837,
+ -0.67355, 0.69686, -0.52799, -0.88857, 0.17480,
+ -0.43255, -0.10468, -0.26964, -0.62339, -0.01929,
+ 0.11779, -0.30509, 0.32977, -0.10731, -0.21553,
+ 0.85621, 0.02098, -0.14388, 0.79342, -0.30795,
+ -0.21668, 0.49725, 0.75411, -0.00246, 0.86694,
+ -0.93919, -1.21032, -1.10646, 0.01015, 0.13320,
+ 0.55944, -1.29907, -0.63339, -1.24951, -0.17478,
+ 0.49568, 0.14971, 0.26437, -0.50140, 0.41977,
+ 1.03527, 0.67050, -0.20712, -0.08180, -0.38730,
+ -1.52927, -0.65614, -0.93422, 0.26765, -1.18438,
+ -0.80842, -0.05991, -0.07915, 0.27380, 0.59327,
+ -0.10607, 0.15173, -0.34407, 0.77168, 0.09979,
+ -1.66073, 0.26227, 1.15590, -0.10427, 0.38302,
+ -0.45927, 0.39567, -0.92825, 0.54598, 0.10877,
+ -1.26001, -0.59938, -0.30749, 0.85523, 0.15063,
+ -0.98294, 0.30193, -1.66652, -0.06495, -0.43179,
+ 0.29549, 0.51482, 0.54981, -0.70457, -0.26832,
+ 0.16275, -0.53499, -0.08106, -0.38393, -0.79100,
+ -1.10553, 0.34671, 0.59053, 0.56584, -0.35012,
+ -0.92151, -0.35571, -0.13222, 0.14160, -0.50967,
+ -2.17800, -0.00545, 0.75297, -1.05801, -0.55743,
+ 0.88938, 1.00124, -0.07126, -0.27972, 0.89254,
+ -0.06308, -1.03097, 0.71459, -0.94045, -0.81828,
+ -0.03809, -0.54499, -0.24873, -1.01063, 0.03461,
+ 1.35690, -0.00429, -0.17794, -0.82302, 0.01950,
+ 0.00940, 0.05580, -0.45424, 0.29664, 0.04604,
+ -0.52540, 0.87988, -0.00783, -0.45943, -0.59419,
+ -0.10473, -0.15874, 0.00921, -1.37827, 0.30850,
+ -0.75548, 0.81571, 0.01202, -0.43698, -0.16643,
+ 0.71028, 1.72127, 0.38465, -0.71813, 1.19139,
+ -1.05091, -0.40939, -0.88229, -0.93050, -1.32913,
+ 0.93106, 0.21027, -0.30906, -0.76101, -0.37449,
+ 0.37803, 0.14400, -1.31750, -0.45545, 0.49401,
+ 0.33637, -0.62988, -0.43635, 0.07933, -0.89059,
+ 0.28543, -1.22112, -1.08938, -0.09242, 0.13417,
+ 0.09742, 0.12138, -0.03681, -0.83756, -0.44282,
+ 0.32800, 1.06358, 0.19999, 0.18985, -3.20328,
+ 0.24759, -0.27644, -0.01948, -0.24044, -0.25442,
+ 0.29513, -1.34057, 0.52548, 1.30572, -1.30789,
+ 0.50417, 1.37292, -0.50537, -1.06767, -0.61078,
+ -1.00487, 0.42099, -0.71185, 1.15723, -0.75580,
+ -0.73691, 0.74631, -0.12611, 0.37938, 0.17827,
+ 0.01106, -0.10640, -0.98341, 0.32616, 0.89735,
+ -1.23809, 0.37315, 0.39033, -0.11397, 0.09591,
+ -0.49401, -1.44079, -2.33540, -0.31666, 0.72371,
+ -0.15273, -0.41721, -0.12445, -0.10986, 0.04234,
+ 0.95950, -0.45056, 0.50729, -0.25767, 0.68841,
+ 1.61424, 0.14794, -0.88035, -0.18776, 0.36890,
+ -0.36944, -1.93983, -0.28332, 0.42254, -0.14904,
+ -1.60961, -0.10590, -0.08659, -0.46802, -0.35255,
+ -0.33921, 1.21704, -0.19500, -0.10241, 0.26305,
+ -0.38169, 0.81578, 0.00921, -0.28171, -0.89682,
+ 0.31154, 0.56288, -1.39025, -0.34601, 0.40992,
+ -1.62191, -0.38283, 0.77870, -1.21307, -0.06334,
+ 1.11182, 0.60496, -0.42626, -0.05700, 0.69720,
+ 0.03808, 0.11749, 0.11970, 0.15078, -0.74303,
+ -0.23312, -0.50700, -0.34149, -2.89814, -0.94659,
+ -0.26546, 0.18373, 1.01093, 0.17713, -0.33360,
+ 1.02726, 0.16475, -0.32958, 0.14524, 1.00910,
+ -0.15319, 0.28561, -1.08271, 0.34289, 1.41081,
+ 0.15333, -1.23957, -0.37187, 0.14183, -1.07646,
+ -1.03572, 0.34050, -1.45848, -0.21968, -1.31931,
+ 0.06203, 0.94795, -0.03255, 1.19056, -0.84562,
+ 0.54079, -0.09154, 0.79826, -0.32462, 0.66799,
+ -0.09316, -0.14355, -0.67540, 0.27681, -0.53594,
+ -1.72983, 0.20131, 0.03270, -1.04085, -0.78548,
+ -0.88503, -0.27611, 1.69764, -0.26504, 0.22760,
+ 0.56582, 0.55247, 0.66397, -0.30659, -0.58562,
+ 0.37722, 0.26361, 0.62085, 0.32341, -0.54094,
+ -0.12033, -1.41677, 0.66976, -2.18998, -1.23484,
+ 0.40933, -2.12217, -0.19272, -0.09467, 1.16538,
+ -0.12910, 0.57050, 1.78121, 1.70032, 0.19060,
+ -0.05668, 0.33148, 0.07828, -0.02690, -0.11815,
+ -0.86589, 0.16739, -2.32581, -1.97742, -2.20262,
+ -1.35388, 0.56841, 0.26790, -0.27363, -0.60873,
+ 0.34891, 0.79625, 0.03954, 0.51874, 1.05827,
+ 1.17348, -0.60927, -0.98074, 0.86436, -0.02351,
+ -1.23545, -0.98910, -0.36018, -0.88461, -0.85903,
+ 0.42677, -0.50148, -0.03557, -0.44191, 0.10000,
+ -0.24597, -0.23699, 0.09688, -1.26611, 0.96955,
+ 0.29935, 0.65235, 0.00702, -0.09714, 0.40060,
+ -0.39432, -0.10631, 0.59712, -2.03541, -0.39459,
+ -0.81183, 0.69800, 1.09149, -1.81730, 0.43079,
+ -0.84042, 0.15955, 0.02730, 0.35249, -0.28777,
+ 0.78812, 0.15303, -0.17654, -1.96923, 0.45451,
+ 0.52748, 1.18484, -0.31354, -0.63898, -0.53305,
+ -0.20382, -0.57215, 0.18186, -0.46893, -0.89780,
+ -0.35257, -0.01811, 0.30921, -0.64254, -0.81544,
+ 0.10879, 0.29388, -0.39497, -0.59281, -0.56777,
+ -0.54728, 0.61235, -0.17225, 0.76725, 0.25044,
+ -0.25309, -0.41273, -0.24776, 0.32029, -0.73334,
+ -0.09763, -0.77728, -0.41058, -0.28951, 0.67728,
+ 0.17805, 0.74961, -0.46418, -0.84614, 1.19043,
+ -0.01578, -0.59582, -0.21538, -0.58797, -0.13734,
+ -1.58407, 0.18549, 0.33481, -0.56066, 0.63146,
+ -0.79844, -0.53596, -0.21997, -0.09921, -0.08722,
+ -0.55010, 0.36538, -0.42723, -0.34363, -0.58709,
+ -0.71161, 0.03472, 0.69408, -0.14608, 0.19702,
+ -0.62483, 0.47503, -0.29023, -0.04817, -0.74586,
+ -0.98852, 0.33637, -0.10023, -0.12365, -0.13141,
+ -0.25397, 1.10090, 0.06783, -0.39030, 0.49296,
+ -0.71007, -1.02657, -2.01177, -0.76459, 1.06431,
+ 1.40526, -0.66825, -0.12610, -0.61593, -1.01682,
+ -0.66249, -0.56630, 0.55659, -0.31557, -0.54861,
+ 0.98620, -1.31174, -0.04871, 0.80169, -0.94208,
+ -0.09026, -0.03376, 0.08043, 0.24564, -0.12058,
+ 0.23180, 0.15589, 0.61135, -0.44232, -1.11003,
+ -1.12400, -0.46581, -0.32226, -1.00883, 0.59600,
+ -0.45052, 0.74476, 0.26735, 0.10657, 0.50324,
+ 0.65667, 0.12144, -0.05788, -0.69543, -0.91906,
+ 0.16916, -0.68633, -1.54501, -1.12662, 0.11306,
+ -0.26834, -0.06807, 0.28808, 0.32572, -0.75926,
+ 0.10769, 0.27329, -0.60959, 0.66760, 0.82301,
+ -0.82904, -0.44364, 1.16048, -1.60537, -0.48613,
+ 0.59681, 0.15080, 0.47346, 0.02886, -0.63198,
+ -0.65340, 0.71999, 0.07769, 0.04906, -1.75672,
+ 0.04548, 0.51854, -1.01889, -1.08982, -3.00298,
+ 0.12043, -0.45009, -1.93552, 0.47792, 0.04859,
+ 0.88398, 0.69290, -0.18265, 0.23184, 0.01391,
+ 0.01582, -0.01571, 0.29586, 0.28784, -1.69579,
+ 0.27455, -0.82223, 0.11279, 0.26675, 0.33287,
+ -1.39928, -0.07239, -1.73255, -0.20557, -0.57492,
+ -0.07915, -0.51987, -0.38600, 1.19755, 0.21372,
+ 0.49170, -0.71723, 0.34488, -2.21927, 0.52643,
+ -1.00133, -0.28252, 1.18919, 0.87096, -0.26989,
+ -0.49666, 1.07759, -1.08545, -0.60889, 0.39556,
+ 0.80877, -1.21813, -0.54140, 0.48162, -0.31063,
+ 0.01020, 0.11088, -0.74460, -0.67461, 0.30461,
+ 0.27401, -0.03308, -0.80455, 0.31687, 0.64951,
+ -0.23626, 0.14127, -0.48103, -0.98248, 1.54022,
+ 1.03098, 0.51832, -0.41475, 0.89839, -0.21923,
+ 0.03634, 0.89437, -0.40895, -0.15344, -0.25787,
+ -0.55204, -0.97091, -1.41252, -0.55219, -0.46681,
+ 0.53244, -1.21085, 0.23461, -0.72897, 0.69331,
+ 0.33023, -0.90804, -0.20939, 0.26997, -0.07019,
+ 0.54684, 0.43599, 1.04665, 0.85356, -0.13619,
+ -0.58017, 0.42337, 0.07710, -2.39141, -1.60395,
+ -0.53071, -1.26377, -0.56941, 0.29571, -0.15469,
+ 0.43872, -1.65017, -0.28216, 0.48608, -1.25389,
+ -0.25430, 0.17832, 0.13532, -0.01488, -0.21711,
+ -0.34775, 0.65302, 0.38700, 0.26095, -2.70865,
+ -0.27671, 0.32918, 0.28252, 1.05826, 0.27267,
+ -0.32170, 0.79501, 1.25519, 0.08360, 0.75010,
+ -0.31676, 0.23804, 1.43980, -0.24084, 0.20951,
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+ -2.35096, -0.33976, 0.41869, -0.69227, -0.10000,
+ 0.26516, -0.71920, 0.41779, -0.61815, -0.72884,
+ -0.55815, -0.20918, -0.36300, -1.95259, -0.25999,
+ 1.36403, 0.15381, -1.53545, -0.30393, -1.83111,
+ 0.66733, 0.81067, 0.72182, 0.09691, -0.33986,
+ 0.43422, -0.89848, -1.22482, -0.24885, -0.10893,
+ -0.57849, 0.74425, -0.60656, -1.01828, 0.08442,
+ 0.41332, 0.46415, -0.27569, -0.24103, 0.47526,
+ 0.18209, -0.50189, -0.47229, -0.38944, 0.92049,
+ 0.26477, 0.12824, -0.54814, 0.28103, -0.87099,
+ -1.28791, 0.37221, 0.00968, 0.32602, -0.82186,
+ 0.38194, 0.29246, 0.42641, 0.31311, 0.20568,
+ -0.39876, -0.46861, -0.96960, -0.29132, -0.68650,
+ 0.38587, -0.89939, 0.36095, -0.84515, -1.19016,
+ -0.53346, -0.32510, -0.27223, -0.60163, 0.38436,
+ 0.40078, -1.86870, -0.20338, -0.67204, 0.17113,
+ 0.16096, -0.01295, 0.74441, 0.03974, 1.12728,
+ 0.00299, 0.32588, 0.36945, 0.11011, -0.86109,
+ -1.23481, 0.25094, -0.37994, -0.90454, 0.56825,
+ -0.50801, -0.66914, -0.28857, 0.69775, -0.31160,
+ 1.38989, -0.60282, -0.46592, 0.92059, 0.94248,
+ -0.07301, -2.09886, 0.02315, 0.12796, -0.41042,
+ -0.28159, -0.17586, 0.05524, -0.12912, -0.13676,
+ 0.28207, -0.68057, 0.63544, 0.17407, -0.18678,
+ -0.29764, -0.40597, -0.01752, 0.24992, 0.28521,
+ -0.31518, 0.16611, -1.42761, -0.58463, -0.34830,
+ -0.34831, -0.66319, -0.09349, 1.03071, -0.45448,
+ 0.48979, -1.04078, 0.36765, -0.60678, -0.41179,
+ -0.44369, -0.79483, -0.26697, -0.70339, -1.55662,
+ 0.93995, 1.10414, 0.15027, 0.71192, 0.20499,
+ -0.33990, -1.11116, 1.46576, -0.24134, -0.70155,
+ 0.50740, -0.72645, -0.15868, -0.69604, 0.20821,
+ -1.70575, 0.36549, -0.51878, 1.42818, 0.24553,
+ 0.16580, -0.81447, 0.56246, -0.10578, -2.13550,
+ 0.48777, 0.16598, -1.08593, -0.74275, 0.84402,
+ -0.73219, 0.03507, 0.47698, 0.18246, -0.26687,
+ 0.79872, -0.56713, -0.16669, -0.69975, -1.01667,
+ 0.10927, 0.16055, -0.65455, -0.28955, -0.33500,
+ 0.61381, -0.43916, 0.11059, -0.90887, -3.28810,
+ 0.07017, 0.03811, -0.87536, 1.43753, -0.13779,
+ -0.36133, -0.35768, -0.21034, -0.55494, 0.73978,
+ -1.00430, -0.24951, -0.97358, -0.40444, 0.56330,
+ -0.69002, 0.36948, -0.37845, -0.73333, -0.12835,
+ 1.12310, 0.05684, -0.01306, -0.08428, -0.18259,
+ -1.19796, 0.12731, -0.88371, 1.22190, 0.05075,
+ 0.36334, 0.34335, 0.37270, -0.20260, -0.34819,
+ -0.56674, 1.05218, -0.45792, -1.42964, -0.90682,
+ -0.30462, 0.27180, 0.26452, -0.28502, 1.03123,
+ 0.26758, -0.61278, 0.11411, 0.70063, 0.35265,
+ 0.82544, -0.29467, -0.53326, -0.33827, 0.11936,
+ 0.21036, -1.64895, -1.24886, -0.20786, -0.78254,
+ -0.33489, 0.14271, -1.25942, 1.08560, 0.10930,
+ 0.50666, 0.93610, -1.84242, -0.32555, 0.19497,
+ 1.51690, -1.19361, -0.47876, -0.05379, 0.41637,
+ -1.29998, -1.49078, -1.19762, 1.32325, -0.32655,
+ -1.01129, 0.61824, -0.31982, -0.48517, -0.31876,
+ 0.30888, 0.06882, -1.09984, -0.07887, -0.92676,
+ -0.72530, 0.33975, 1.51855, -1.28659, 0.20747,
+ 0.27251, 1.07868, -0.84783, -0.11148, -0.59650,
+ -0.56027, -1.21462, 0.44186, 0.28131, 0.73099,
+ 0.95940, 0.66055, 0.81866, -0.37329, -0.11396,
+ 0.57080, -0.24588, 0.42724, -0.29657, -0.92274,
+ -0.73017, 0.39107, -0.46857, 0.48033, -1.29219,
+ -2.37970, -1.32016, 0.82912, 0.31479, -1.40773,
+ 0.58103, -0.86531, 0.01979, 0.00053, 0.35300,
+ 0.59825, 0.22807, -0.69291, -1.09691, 0.10843,
+ -0.02597, -0.79435, -0.15086, 0.01818, -0.53372,
+ 0.66544, -0.42290, -0.32938, -0.52015, 0.22640,
+ -0.21689, 0.11334, -0.65610, 0.68462, 0.42183,
+ -0.11446, 0.14970, 0.67565, 1.55920, -0.98156,
+ 0.24228, -1.06309, -0.41398, 0.03149, 0.49234,
+ -1.67691, -0.01619, -0.65993, -0.49266, 0.14015,
+ -1.18998, 0.11452, 0.23510, -1.54204, -0.26392,
+ -1.62562, 0.09447, -0.67027, -0.83244, -0.08166,
+ 0.63546, -1.71853, -1.08750, 0.10638, 1.31132,
+ 0.35845, 0.30748, 0.57238, 0.68576, 0.69511,
+ 0.40000, -0.73227, -0.59980, 0.66928, -2.21755,
+ -1.31317, -0.96778, 0.89564, -0.69360, -0.32379,
+ -0.74453, -1.40262, -1.20561, 0.12335, -0.08899,
+ 0.26665, -0.08525, 0.20390, 0.46269, 1.02856,
+ 0.59654, 0.96756, -0.12789, 1.80793, -0.10000,
+ -0.30349, -0.15009, -1.23132, -0.26989, -0.31716,
+ 0.04892, 1.29807, -0.83743, 0.22960, -1.20981,
+ 1.07244, 0.21850, -0.16992, -0.22858, -0.20182,
+ 0.10639, -0.52359, -0.65887, 0.15727, -0.21683,
+ 0.26967, -1.56153, 1.02571, -0.37055, -0.12119,
+ 0.43586, -0.09238, 0.41842, 1.09008, -0.78701,
+ -0.42469, -0.63264, -0.15225, -1.19488, -0.33759,
+ 0.51075, 0.84622, -0.88941, -0.14295, -0.51913,
+ -0.16640, -0.05239, 0.76396, 0.71249, -0.32561,
+ 0.49246, 0.37483, -0.88159, -0.07772, -1.69652,
+ -0.05901, -0.37812, -0.19769, -0.44073, -0.24106,
+ 0.29540, 1.14272, 0.26810, -1.45417, -0.34369,
+ 0.37022, -0.56089, -0.48137, 0.07160, 0.56546,
+ 0.12776, 0.29948, 0.28995, 0.96108, 0.46839,
+ -0.56657, -0.16532, -0.24438, -0.76014, -0.84063,
+ -2.18691, 0.06781, 0.56740, -0.16623, -0.57653,
+ -0.77040, -0.20381, 0.59543, -0.25137, -1.43976,
+ -1.22344, -0.15204, -0.42566, -1.81867, 0.51080,
+ 0.64111, -0.32440, -1.64334, 0.05293, 0.14532,
+ 1.44147, -0.63060, -0.15590, 0.88374, 0.65466,
+ 0.09433, -0.09729, 0.50433, 1.32396, -1.05955,
+ 0.20557, -0.77897, -0.73206, -0.04303, -0.14055,
+ -0.05144, -0.58804, -1.10292, -0.20940, 0.25209,
+ -0.02096, -0.29672, -0.67392, 0.47134, 0.58825,
+ 0.18208, -0.77245, -0.24338, 0.11579, -0.43047,
+ -0.04863, -1.29924, -0.47345, -0.33874, 0.50527,
+ -1.88350, 0.65906, 0.23723, -0.28698, -0.73835,
+ -0.56176, -0.64539, -0.37396, -0.32286, 0.19575,
+ 0.35936, 0.40669, -0.60229, 1.23450, -0.09061,
+ -0.04838, 0.34969, 0.38917, -0.51357, -0.60398,
+ 1.32366, 0.09287, -0.98066, -0.85120, -0.78697,
+ -0.50539, 0.43478, -0.50898, 0.33395, 0.28632,
+ -0.77964, 0.48608, 0.31149, -0.14590, 0.76181,
+ -0.63158, -1.04415, 0.01392, 0.37278, -2.11654,
+ -0.43194, 0.16968, 0.34019, -0.06137, 0.57454,
+ 0.66506, -0.66367, -0.31304, 0.23035, 0.00274,
+ 0.32365, -1.22979, -0.11079, 0.42036, 0.06991,
+ -1.35240, -0.39349, 0.32384, -0.13804, -2.91808,
+ 2.30108, -1.51842, -1.67079, -3.11120, 1.49528,
+ 1.37863, -1.75063, -1.69591, -1.49327, 1.06363,
+ 1.47514, -1.47938, -2.05533, -1.50862, -1.89543,
+ 1.78557, 1.62051, -1.56852, -1.36052, 1.43622,
+ -1.20130, 1.48415, 1.38946, 1.28286, 1.10223,
+ 1.88459, 1.55920, -1.79075, 1.72101, 1.81805,
+ -0.29259, -2.30108, 1.51842, 1.67079, 3.11121,
+ -1.49529, -1.37863, 1.75063, 1.69590, 1.49327,
+ -1.06363, -1.47514, 1.47937, 2.05534, 1.50863,
+ 1.89544, -1.78557, -1.62051, 1.56851, 1.36051,
+ -1.43622, 1.20129, -1.48415, -1.38947, -1.28284,
+ -1.10223, -1.88459, -1.55920, 1.79076, -1.72101,
+ -1.81807, 0.29259,
+};
--- /dev/null
+> Foobar_dundeefriends
+# RESIDUE COILS REM465 HOTLOOPS
+M 0.86010 0.88512 0.37094
+T 0.79983 0.85864 0.44331
+A 0.72031 0.83329 0.42744
+D 0.62168 0.79393 0.24390
+G 0.50983 0.59080 0.11673
+P 0.25998 0.36247 0.06320
+R 0.29879 0.44037 0.06982
+E 0.25286 0.32959 0.05194
+L 0.21085 0.31715 0.04783
+L 0.17763 0.27760 0.02311
+Q 0.16044 0.27182 0.01845
+L 0.18476 0.27532 0.04620
+R 0.22259 0.29066 0.06996
+A 0.26044 0.31137 0.08420
+A 0.28021 0.31834 0.09161
+V 0.31770 0.33024 0.09771
+R 0.34459 0.33123 0.10017
+H 0.35438 0.33015 0.10042
+R 0.34941 0.31879 0.09479
+P 0.33860 0.29840 0.08436
+Q 0.31280 0.26756 0.07276
+D 0.27741 0.22690 0.06044
+F 0.25835 0.18412 0.05193
+V 0.22091 0.15604 0.03427
+A 0.19781 0.13840 0.02145
+W 0.17252 0.12069 0.00934
+L 0.16471 0.13344 0.00824
+M 0.18962 0.14399 0.02030
+L 0.20990 0.15715 0.02233
+A 0.24890 0.18675 0.02482
+D 0.30416 0.20404 0.02828
+A 0.36864 0.21878 0.03293
+E 0.42323 0.24384 0.03802
+L 0.49613 0.27329 0.04467
+G 0.54673 0.30276 0.04821
+M 0.58288 0.32961 0.05112
+G 0.58734 0.35779 0.05103
+D 0.57351 0.39639 0.04991
+T 0.54838 0.40374 0.04728
+T 0.49719 0.41796 0.04257
+A 0.44247 0.42299 0.03589
+G 0.38488 0.42355 0.03230
+E 0.32062 0.43459 0.02845
+M 0.27621 0.43599 0.02370
+A 0.24947 0.43579 0.02298
+V 0.26104 0.44630 0.02480
+Q 0.28555 0.42657 0.02998
+R 0.33863 0.41808 0.03700
+G 0.42083 0.41277 0.04747
+L 0.52012 0.40903 0.05937
+A 0.57192 0.40310 0.06615
+L 0.61014 0.39172 0.07155
+H 0.62000 0.38603 0.07143
+P 0.61420 0.38863 0.07132
+G 0.59027 0.36809 0.06880
+H 0.54439 0.37383 0.06386
+P 0.50222 0.36429 0.05768
+E 0.45498 0.35329 0.05279
+A 0.40408 0.33619 0.04550
+V 0.36729 0.33364 0.03718
+A 0.33908 0.34380 0.03627
+R 0.34141 0.35219 0.03640
+L 0.35060 0.35611 0.03942
+G 0.37329 0.36835 0.04165
+R 0.39930 0.37477 0.04556
+V 0.41249 0.38955 0.04707
+R 0.40000 0.39924 0.04544
+W 0.38778 0.41158 0.04330
+T 0.36202 0.43951 0.03890
+Q 0.32894 0.45950 0.03453
+Q 0.29139 0.46461 0.03096
+R 0.24944 0.47555 0.02594
+H 0.22078 0.46457 0.02235
+A 0.18668 0.44830 0.01686
+E 0.15893 0.41673 0.01509
+A 0.13593 0.41862 0.01529
+A 0.13590 0.41297 0.02241
+V 0.16183 0.39515 0.02782
+L 0.19353 0.40028 0.03466
+L 0.24663 0.40988 0.04213
+Q 0.31725 0.43753 0.04908
+Q 0.38948 0.45652 0.05581
+A 0.46684 0.49088 0.06222
+S 0.54056 0.51927 0.06666
+D 0.60106 0.54082 0.06870
+A 0.64620 0.53213 0.06829
+A 0.66751 0.51461 0.06782
+P 0.65871 0.48304 0.06293
+E 0.61353 0.45002 0.05575
+H 0.54564 0.40062 0.04662
+P 0.48933 0.35331 0.04148
+G 0.42808 0.30441 0.03594
+I 0.39194 0.24590 0.03330
+A 0.35118 0.18098 0.02877
+L 0.33052 0.16960 0.02819
+W 0.32568 0.16924 0.02737
+L 0.32371 0.18936 0.02656
+G 0.33488 0.20189 0.02826
+H 0.35178 0.23060 0.02991
+A 0.36475 0.26267 0.03080
+L 0.36778 0.29931 0.03102
+E 0.35647 0.34612 0.03008
+D 0.32886 0.40965 0.02761
+A 0.28835 0.44616 0.02340
+G 0.22931 0.48443 0.01894
+Q 0.19242 0.49768 0.01648
+A 0.17246 0.51975 0.01495
+E 0.14513 0.52485 0.01265
+A 0.14509 0.52733 0.01241
+A 0.13113 0.52307 0.01172
+A 0.14257 0.52022 0.00727
+A 0.15732 0.49780 0.00925
+A 0.16228 0.47742 0.01891
+Y 0.19799 0.44287 0.03106
+T 0.24619 0.40365 0.03941
+R 0.30467 0.37339 0.05366
+A 0.38077 0.34312 0.06721
+H 0.44188 0.32533 0.07549
+Q 0.49887 0.30498 0.07979
+L 0.56428 0.26520 0.08702
+L 0.60765 0.24710 0.09515
+P 0.62855 0.22427 0.09743
+E 0.61894 0.22200 0.09484
+E 0.59193 0.21352 0.08797
+P 0.55817 0.21264 0.07919
+Y 0.50412 0.20699 0.06826
+I 0.45257 0.20568 0.05530
+T 0.38361 0.21586 0.05098
+A 0.31311 0.22920 0.04859
+Q 0.25850 0.23918 0.04120
+L 0.22610 0.24305 0.03398
+L 0.20761 0.24496 0.03393
+N 0.21606 0.24725 0.03076
+W 0.21665 0.23931 0.02528
+R 0.24919 0.22444 0.02444
+R 0.29430 0.21166 0.02930
+R 0.31798 0.20457 0.03067
+L 0.33694 0.18726 0.03113
+C 0.34845 0.17414 0.03145
+D 0.36210 0.16875 0.03166
+W 0.37031 0.16887 0.03294
+R 0.37025 0.16619 0.03378
+A 0.35790 0.18814 0.03081
+L 0.33779 0.21887 0.03011
+D 0.30930 0.24621 0.02892
+V 0.26754 0.27678 0.02676
+L 0.23659 0.32224 0.02315
+S 0.20691 0.35984 0.02471
+A 0.17775 0.39641 0.02215
+Q 0.15081 0.42204 0.02329
+V 0.14823 0.43457 0.02579
+R 0.15588 0.44450 0.02810
+A 0.18517 0.44995 0.03299
+A 0.22282 0.44130 0.03871
+V 0.26328 0.41804 0.04349
+A 0.31092 0.40182 0.04799
+Q 0.35060 0.36068 0.05071
+G 0.38352 0.32101 0.05107
+V 0.42164 0.29133 0.05083
+G 0.45736 0.26373 0.05326
+A 0.49886 0.22661 0.05499
+V 0.52391 0.20562 0.05560
+E 0.53303 0.20165 0.05326
+P 0.53975 0.20063 0.05487
+F 0.52385 0.20385 0.05015
+A 0.50639 0.22752 0.05004
+F 0.48741 0.26114 0.04785
+L 0.46674 0.28999 0.04586
+S 0.43909 0.33263 0.04388
+E 0.39696 0.36707 0.03940
+D 0.35208 0.41809 0.03515
+A 0.30408 0.46253 0.03007
+S 0.24901 0.46649 0.02454
+A 0.19867 0.47834 0.01929
+A 0.16075 0.50072 0.01365
+E 0.13788 0.50748 0.01122
+Q 0.13506 0.50876 0.01368
+L 0.12169 0.51337 0.01547
+A 0.12136 0.51136 0.01598
+C 0.13259 0.50633 0.01649
+A 0.13448 0.48088 0.01786
+R 0.13417 0.48245 0.02171
+T 0.14810 0.47380 0.02092
+R 0.15594 0.46796 0.02898
+A 0.16180 0.47356 0.03389
+Q 0.19117 0.47436 0.04219
+A 0.22511 0.46346 0.05995
+I 0.26575 0.46364 0.06867
+A 0.31723 0.44786 0.08230
+A 0.37505 0.45856 0.10196
+S 0.43341 0.46499 0.12734
+V 0.50181 0.46517 0.14401
+R 0.55621 0.45469 0.15645
+P 0.60375 0.45290 0.17581
+L 0.64486 0.44417 0.18570
+A 0.66990 0.43379 0.19070
+P 0.68382 0.41168 0.18878
+T 0.70233 0.41020 0.18048
+R 0.72070 0.40484 0.16987
+V 0.71180 0.39972 0.16069
+R 0.71532 0.37964 0.14413
+S 0.70293 0.35656 0.12867
+K 0.67155 0.32107 0.11402
+G 0.63844 0.31759 0.08838
+P 0.61151 0.28482 0.07748
+L 0.58165 0.26357 0.07057
+R 0.56607 0.23944 0.06683
+V 0.55583 0.20985 0.05244
+G 0.54798 0.18271 0.04783
+F 0.54729 0.18625 0.06066
+V 0.56353 0.19115 0.06687
+S 0.58514 0.20302 0.07328
+N 0.61899 0.21760 0.07727
+G 0.64417 0.24094 0.08164
+F 0.66852 0.25410 0.08724
+G 0.67113 0.26439 0.08635
+A 0.65329 0.26395 0.08354
+H 0.59906 0.25471 0.07613
+P 0.53852 0.23852 0.06676
+T 0.46756 0.23838 0.05520
+G 0.39638 0.22887 0.04532
+L 0.32435 0.21985 0.03424
+L 0.25959 0.20622 0.02455
+T 0.21092 0.19002 0.01454
+V 0.16286 0.18984 0.00874
+A 0.13222 0.19663 0.01040
+L 0.13718 0.21327 0.01176
+F 0.15922 0.22668 0.01421
+E 0.19287 0.25014 0.01571
+A 0.24795 0.27481 0.02231
+L 0.30912 0.29319 0.02781
+Q 0.36600 0.31761 0.03436
+R 0.40904 0.32357 0.04039
+R 0.44641 0.31944 0.04550
+Q 0.47387 0.31066 0.04911
+P 0.48015 0.30088 0.05001
+D 0.46585 0.27977 0.04718
+L 0.43848 0.26224 0.04029
+Q 0.41204 0.24283 0.03653
+M 0.40286 0.22376 0.03416
+H 0.38445 0.22935 0.04559
+L 0.40616 0.24686 0.05506
+F 0.44756 0.28038 0.07106
+A 0.47610 0.30637 0.08409
+T 0.52735 0.35044 0.09517
+S 0.56587 0.38896 0.10535
+G 0.57757 0.43154 0.10837
+D 0.58300 0.46681 0.10980
+D 0.55714 0.47586 0.10507
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+> dundeefriends
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git://source.jalview.org / jabaws.git / commitdiff