[med-svn] [Git][med-team/bitseq][master] 6 commits: Use 2to3 to port scripts to Python3
Andreas Tille
gitlab at salsa.debian.org
Sun Sep 1 06:59:23 BST 2019
Andreas Tille pushed to branch master at Debian Med / bitseq
Commits:
39d9e842 by Andreas Tille at 2019-09-01T05:46:02Z
Use 2to3 to port scripts to Python3
- - - - -
c613406b by Andreas Tille at 2019-09-01T05:46:18Z
debhelper-compat 12
- - - - -
f9bd6824 by Andreas Tille at 2019-09-01T05:46:21Z
Standards-Version: 4.4.0
- - - - -
8dc7aa7d by Andreas Tille at 2019-09-01T05:46:22Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
996f1f60 by Andreas Tille at 2019-09-01T05:54:33Z
Build-Depends: python3
- - - - -
e6947ad9 by Andreas Tille at 2019-09-01T05:57:56Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+bitseq (0.7.5+dfsg-5) unstable; urgency=medium
+
+ * Use 2to3 to port scripts to Python3
+ Closes: #936209
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Trim trailing whitespace.
+
+ -- Andreas Tille <tille at debian.org> Sun, 01 Sep 2019 07:54:49 +0200
+
bitseq (0.7.5+dfsg-4) unstable; urgency=medium
[ Graham Inggs ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,14 +4,14 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
zlib1g-dev,
libbam-dev,
libboost-dev,
help2man,
- python,
- python-numpy
-Standards-Version: 4.2.1
+ python3,
+ python3-numpy
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/bitseq
Vcs-Git: https://salsa.debian.org/med-team/bitseq.git
Homepage: https://github.com/BitSeq/BitSeq
@@ -20,7 +20,8 @@ Package: bitseq
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- python
+ python3,
+ python3-numpy
Suggests: samtools
Description: Bayesian Inference of Transcripts from Sequencing Data
BitSeq is an application for inferring expression levels of individual
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,256 @@
+Description: Use 2to3 to port scripts to Python3
+Bug-Debian: https://bugs.debian.org/936209
+Author: Andreas Tille <tille at debian.org>
+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();
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ hardening.patch
fix_clean_target.patch
spelling.patch
fix_build_options.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -76,5 +76,3 @@ override_dh_auto_install:
if [ "$${bscript}" = "parseAlignment.py" ] ; then continue ; fi ; \
ln -s $(debianmedsysdir)/$${bscript} $(bindir)/`echo $${bscript} | sed -e 's/\.py$$//' -e 's/\.sh$$//'` ; \
done
-
-
View it on GitLab: https://salsa.debian.org/med-team/bitseq/compare/ee0c5d03c823008d84154aa9af9633aba3342971...e6947ad914fb8b11305db190c03e64bd6fc348ce
--
View it on GitLab: https://salsa.debian.org/med-team/bitseq/compare/ee0c5d03c823008d84154aa9af9633aba3342971...e6947ad914fb8b11305db190c03e64bd6fc348ce
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