Delete unneeded directory
[jabaws.git] / website / archive / binaries / mac / src / disembl / DisEMBL.py.original
diff --git a/website/archive/binaries/mac/src/disembl/DisEMBL.py.original b/website/archive/binaries/mac/src/disembl/DisEMBL.py.original
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-#!/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()