X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fdisembl%2FDisEMBL.py;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fdisembl%2FDisEMBL.py;h=0000000000000000000000000000000000000000;hb=fb21789ba11ae9b9f6abed1b01d4542e54abfe34;hp=7298e8377c0981ad6e6d320c7c446b590d1ab166;hpb=7d68cf3489c816b2ed7afb1925a6de2168eccf4a;p=jabaws.git

diff --git a/website/archive/binaries/mac/src/disembl/DisEMBL.py b/website/archive/binaries/mac/src/disembl/DisEMBL.py
deleted file mode 100644
index 7298e83..0000000
--- a/website/archive/binaries/mac/src/disembl/DisEMBL.py
+++ /dev/null
@@ -1,172 +0,0 @@
-#!/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 = 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) )
-           
-    print ''
-
-
-
-def runDisEMBLpipeline():
-    try:
-        smooth_frame = 8
-        peak_frame = 8
-        join_frame = 4
-        fold_coils = 1.2
-        fold_hotloops = 1.4
-        fold_rem465 = 1.2
-        mode = 'scores'
-        try:
-            file = open(sys.argv[1],'r')
-        except:
-            mode = 'default'
-    except:
-        print '\nDisEMBL.py sequence_file \n'
-        print 'A default run would be: ./DisEMBL.py fasta_file'
-        raise SystemExit
-    #db = sys.stdin
-    parser = Fasta.RecordParser()
-    iterator = Fasta.Iterator(file,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)
-
-            sys.stdout.write('> '+cur_record.title+'\n')
-            sys.stdout.write('# COILS ')
-            reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
-            sys.stdout.write('# REM465 ')
-            reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
-            sys.stdout.write('# HOTLOOPS ')
-            reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
-            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')
-        except AttributeError:
-            break
-    file.close()
-    return
-
-runDisEMBLpipeline()