Description: Use 2to3 to port scripts to Python3 Bug-Debian: https://bugs.debian.org/936209 Author: Andreas Tille Last-Update: Sun, 01 Sep 2019 07:43:45 +0200 --- a/checkTR.py +++ b/checkTR.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 """ Due to an error in our code, GENE EXPRESSION and WITHIN GENE EXPRESSION results @@ -53,14 +53,14 @@ def checkFile(fileName): if len(genesWrong) == 0: print("Everything seems to be fine.") else: - print("These "+str(len(genesWrong))+" (out of "+str(len(genesSeen))+") have wrong GENE EXPRESSION results:") + print(("These "+str(len(genesWrong))+" (out of "+str(len(genesSeen))+") have wrong GENE EXPRESSION results:")) trCount = 0; genesStr = ""; for it in genesWrong: genesStr += it+" "; trCount+=len(g2ts[it]); print(genesStr); - print("These "+str(trCount)+" transcripts have wrong WITHIN GENE EXPRESSION results:"); + print(("These "+str(trCount)+" transcripts have wrong WITHIN GENE EXPRESSION results:")); trsStr = ""; for it in genesWrong: for trit in g2ts[it]: @@ -70,7 +70,7 @@ def checkFile(fileName): if __name__ == "__main__": if len(sys.argv) <2: sys.exit("Please provide file name as argument."); - print("Checking file "+sys.argv[1]); + print(("Checking file "+sys.argv[1])); checkFile(sys.argv[1]); --- a/extractTranscriptInfo.py +++ b/extractTranscriptInfo.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # Initialization {{{ import sys from optparse import OptionParser @@ -13,7 +13,7 @@ parser.add_option("-t","--type",dest="ty (options, args) = parser.parse_args() def verbose(str): if options.verbose: - print str; + print(str); if len(args)<2: sys.exit("Missing arguments"); @@ -41,16 +41,16 @@ li = 0; if options.type: if options.type=="ensembl": itype = "ens"; - print "Expecting header line format:\n>[tr Name] .* gene:[gene Name] .*"; + print("Expecting header line format:\n>[tr Name] .* gene:[gene Name] .*"); elif options.type=="cuff": itype = "cuf"; - print "Expecting header line format:\n>[tr Name] .* gene=[gene Name] .*"; + print("Expecting header line format:\n>[tr Name] .* gene=[gene Name] .*"); else: itype = "non"; - print "Expecting header line format:\n>[tr Name] .*\n -> using \"none\" as gene names"; + print("Expecting header line format:\n>[tr Name] .*\n -> using \"none\" as gene names"); else: itype = "non"; - print "Expecting header line format:\n>[tr Name] .*\n -> using \"none\" as gene names"; + print("Expecting header line format:\n>[tr Name] .*\n -> using \"none\" as gene names"); for line in inF: li+=1; @@ -64,7 +64,7 @@ for line in inF: seqName = lSplit[0]; if seqName == "": seqName = "unknown-tr"+str(seqCount); - print "Warning: no name on line ",li,". Using '",seqName,"'."; + print("Warning: no name on line ",li,". Using '",seqName,"'."); if itype == "non": geneName = "none"; else: --- a/getCounts.py +++ b/getCounts.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # Initialization {{{ import sys import numpy as np @@ -15,7 +15,7 @@ parser.add_option("-p", "--probDir", des parser.add_option("-n", "--Nmap", dest="Nmap", help = "Comma separated list of total aligned-read-counts for each experiment.",type="string"); def verbose(str): if options.verbose: - print str; + print(str); (options, args) = parser.parse_args() if len(args)==0: @@ -45,12 +45,12 @@ else: inF = open(fn); except: sys.exit("Unable to open file: "+fn); - print "Reading file: ",fn; + print("Reading file: ",fn); Nmap = 0; for line in inF: if line[0]!="#": break; ls=line.split(); - for i in xrange(len(ls)-1): + for i in range(len(ls)-1): if ls[i] == "Nmap": Nmap = int(ls[i+1]); inF.close(); if Nmap <= 0: @@ -59,18 +59,18 @@ else: means = [np.transpose(np.loadtxt(arg))[1] for arg in args]; -print "Files:"; -for j in xrange(len(args)): - print " ",args[j],N[j]; +print("Files:"); +for j in range(len(args)): + print(" ",args[j],N[j]); try: outF = open(options.out,"w"); except: sys.exit("Unable to open output file: ",options.out); -for i in xrange(len(means[0])): - for j in xrange(len(means)): - outF.write(str(long(round(means[j][i]*N[j])))+" "); +for i in range(len(means[0])): + for j in range(len(means)): + outF.write(str(int(round(means[j][i]*N[j])))+" "); outF.write("\n"); outF.close(); --- a/parseAlignment.py +++ b/parseAlignment.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # Initialization {{{ import sys import numpy as np @@ -6,7 +6,7 @@ def normpdf(x,m,s): return 1./(s*2.5066282746310002)*np.exp(-1./(2.0*s*s)*(x-m)**2.) import os, time # needed for this: time_str = time.strftime("%b %e %Y %H:%M:%S", time.gmtime(os.lstat(sys.argv[0]).st_mtime)); -print "###",os.path.basename(sys.argv[0]),"build:",time_str; +print("###",os.path.basename(sys.argv[0]),"build:",time_str); # {{{ parse arguments and set filenames from optparse import OptionParser parser = OptionParser(usage="%prog [options]\n -a -t are necessary\n -e is adviced") @@ -80,7 +80,7 @@ def nuc2i(str):#{{{ #}}} def verbose(str):#{{{ if options.verbose: - print str; + print(str); #}}} verbose("Using files:\n "+aFileName+" for reading alignments\n "+oFileName+" for writing probabilities\n "+tFileName+" for writing transcript info"); # {{{ reading transcript info @@ -178,7 +178,7 @@ if options.inputType=="fasta": #{{{ # while pos >= len(nucProb): # nucProb.append([[pseudoCount for i in range(5)] for k in range(5)]); nucProb[pos][ nuc2 ][ nuc2 ]-=1; - if nucProb[pos][nuc2][nuc2]<1 : print pos,nuc2,seq,mismatch; + if nucProb[pos][nuc2][nuc2]<1 : print(pos,nuc2,seq,mismatch); nucProb[pos][ nuc1 ][ nuc2 ]+=1; # }}} """verbose("Using only unique reads");#{{{ @@ -217,13 +217,13 @@ for line in aFile: nucProb[i][j][k] /= total; if options.veryVerbose: - print "Noise probabilities: "; - print " ",; - print noiseProb; - print "Nucleotide mismatch matrix:"; + print("Noise probabilities: "); + print(" ", end=' '); + print(noiseProb); + print("Nucleotide mismatch matrix:"); for i in range(len(nucProb)): - print "Position ",i,":\n ",; - print nucProb[i]; + print("Position ",i,":\n ", end=' '); + print(nucProb[i]); #}}} verbose("Writing alignment probabilities"); # {{{ aFile.seek(0); @@ -274,7 +274,7 @@ for line in aFile: trans = trMap[ alignment[2+colS][prefixL:] ]; else: trans = 0; - print "Transcript '"+alignment[2+colS]+"' or '"+alignment[2+colS][prefixL:]+"' was not found in the transcript file."; + print("Transcript '"+alignment[2+colS]+"' or '"+alignment[2+colS][prefixL:]+"' was not found in the transcript file."); #print alignment; # calculate probabilities prob=1.0; @@ -313,11 +313,11 @@ else: phredS = float(ord(Q)-Qshift); if phredS<0: if not phredWarning: - print "WARNING: Phred score too low (",int(phredS),") perhpas use --inputType fastq33."; + print("WARNING: Phred score too low (",int(phredS),") perhpas use --inputType fastq33."); phredWarning=True; elif phredS>65: if not phredWarning: - print "NOTE: Phred score unnaturally high (",int(phredS),") check your input type and perhaps set --inputType fastq."; + print("NOTE: Phred score unnaturally high (",int(phredS),") check your input type and perhaps set --inputType fastq."); phredWarning=True; return 1-10**( phredS / -10); def qTOpInvert(Q): @@ -436,7 +436,7 @@ else: trans = trMap[ alignment[2+colS][prefixL:] ]; else: trans = 0; - print "Transcript '"+alignment[2+colS]+"' or '"+alignment[2+colS][prefixL:]+"' was not found in the transcript file."; + print("Transcript '"+alignment[2+colS]+"' or '"+alignment[2+colS][prefixL:]+"' was not found in the transcript file."); #print alignment; # calculate probabilities probLoc = prob; @@ -448,7 +448,7 @@ else: pos = int( mis.split(":")[0] ); except: pos=0; - print 'X',mis,'X',alignment; + print('X',mis,'X',alignment); probLoc = probLoc * qTOpInvert(phread[pos]); if options.paired and len(align2)==columnN: mismatch=align2[columnN-1] @@ -458,7 +458,7 @@ else: pos = int( mis.split(":")[0] ); except: pos=0; - print mis + print(mis) probLoc = probLoc * qTOpInvert(phread2[pos]); # add new alignment to list @@ -477,6 +477,6 @@ else: oFile.write("\n"); -print "Processed:\n ",alN,"alignments + (",readN,"noise alignments)\n ",readN,"reads\n ",trN,"transcripts\nTotal reads: ",Ntotal,"\n"; +print("Processed:\n ",alN,"alignments + (",readN,"noise alignments)\n ",readN,"reads\n ",trN,"transcripts\nTotal reads: ",Ntotal,"\n"); aFile.close(); oFile.close();