[med-svn] [Git][med-team/ssake][master] 9 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Thu Sep 5 13:34:34 BST 2019
Andreas Tille pushed to branch master at Debian Med / ssake
Commits:
6493fabf by Andreas Tille at 2019-09-05T12:26:26Z
Use 2to3 to port to Python3
- - - - -
897b86fb by Andreas Tille at 2019-09-05T12:28:26Z
Build-Depends: markdown instead of python-markdown
- - - - -
eebc6a07 by Andreas Tille at 2019-09-05T12:28:45Z
debhelper-compat 12
- - - - -
185e5f41 by Andreas Tille at 2019-09-05T12:28:51Z
Standards-Version: 4.4.0
- - - - -
482ed6a3 by Andreas Tille at 2019-09-05T12:30:48Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
0bd8e903 by Andreas Tille at 2019-09-05T12:30:49Z
Remove trailing whitespace in debian/changelog
- - - - -
a859d4ef by Andreas Tille at 2019-09-05T12:30:56Z
Set fields Upstream-Name in debian/copyright.
- - - - -
d3c142b3 by Andreas Tille at 2019-09-05T12:30:56Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
84fbc90c by Andreas Tille at 2019-09-05T12:32:55Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+ssake (4.0-3) unstable; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #938561
+ * Build-Depends: markdown instead of python-markdown
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/changelog
+ * Set fields Upstream-Name in debian/copyright.
+ * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Sep 2019 14:30:57 +0200
+
ssake (4.0-2) unstable; urgency=medium
* Fix installation of tools
@@ -81,7 +95,7 @@ ssake (3.8.1-1) unstable; urgency=medium
ssake (3.8-2) unstable; urgency=low
[ A. Costa ]
- * Corrected a typo in debian/ssake.1 (Closes: #650469).
+ * Corrected a typo in debian/ssake.1 (Closes: #650469).
[ Charles Plessy ]
* Depend on libperl4-corelibs-perl | perl (<< 5.12.3-7).
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,9 +4,9 @@ Uploaders: Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
- python-markdown
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12),
+ markdown
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/ssake
Vcs-Git: https://salsa.debian.org/med-team/ssake.git
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake
@@ -15,7 +15,7 @@ Package: ssake
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
- python,
+ python3,
libperl4-corelibs-perl
Suggests: ssake-examples
Description: genomics application for assembling millions of very short DNA sequences
=====================================
debian/copyright
=====================================
@@ -1,5 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/3.8/ssake_v3-8-tar.gz
+Upstream-Name: SSAKE
Files: *
Copyright: © 2006-2018 Canada's Michael Smith Genome Science Centre
@@ -25,4 +26,3 @@ Copyright: © 2008-2018 Andreas Tille <tille at debian.org>
© 2009 Charles Plessy <plessy at debian.org>
License: Same-as-SSAKE-itelf
(see above)
-
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,281 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/938561
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 05 Sep 2019 14:24:24 +0200
+
+--- a/readme.md
++++ b/readme.md
+@@ -188,7 +188,7 @@ SSAKE is implemented in PERL and runs on
+
+ Side-by-side comparison between ssake2.0 and vcake1.0 indicates that SSAKE is nearly 3-fold faster and yields contigs that are as contiguous and accurate.
+
+-The python version 2.0 (released in ssake_v2.0.tar.gz and distributed under ./tools) has not yet been fully tested.
++The python3 version 2.0 (released in ssake_v2.0.tar.gz and distributed under ./tools) has not yet been fully tested.
+ Due to SSAKE's memory requirements, you would need a version
+ of the perl interpreter compiled for 64-bit computers if you intend to assemble millions of short sequences.
+ Development of SSAKE was done using perl v5.8.5 built for x86_64-linux-thread-multi
+--- a/tools/TQS.py
++++ b/tools/TQS.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ __doc__ = """
+ TQS
+@@ -53,18 +53,18 @@ def main():
+ f = open(opts.seqfile)
+ seq = f.readlines()
+ f.close()
+- except Exception, e:
+- print "ERROR: Could not read from %s: %s" % (opts.seqfile, e)
+- print usage % (sys.argv[0:])
++ except Exception as e:
++ print("ERROR: Could not read from %s: %s" % (opts.seqfile, e))
++ print(usage % (sys.argv[0:]))
+ sys.exit()
+
+ try:
+ f = open(opts.qualfile)
+ qual = f.readlines()
+ f.close()
+- except Exception, e:
+- print "ERROR: Could not read from %s: %s" % (opts.qualfile, e)
+- print usage % (sys.argv[0:])
++ except Exception as e:
++ print("ERROR: Could not read from %s: %s" % (opts.qualfile, e))
++ print(usage % (sys.argv[0:]))
+ sys.exit()
+
+
+@@ -75,22 +75,22 @@ def main():
+ try:
+ FASTA = open(fasta, 'w')
+ except:
+- print "ERROR: Can not write to %s" % fasta
++ print("ERROR: Can not write to %s" % fasta)
+ sys.exit()
+
+ try:
+ LOG = open(log, 'w')
+ except:
+- print "ERROR: Can not write to %s" % log
++ print("ERROR: Can not write to %s" % log)
+ sys.exit()
+
+
+ if opts.mer < 15 or opts.mer > 200:
+- print "ERROR: -l must be a number between 15 and 200."
++ print("ERROR: -l must be a number between 15 and 200.")
+ sys.exit()
+
+ if opts.consec < 16 or opts.consec > opts.mer:
+- print "ERROR: -c must be a number between 16 and -l."
++ print("ERROR: -c must be a number between 16 and -l.")
+ sys.exit()
+
+ LOG.write("""
+@@ -130,7 +130,7 @@ def parseQualFile(threshold, difference,
+ read_number = 0
+
+ if verbose:
+- print "Printing trimming pattern for all reads passing the set threshold values...\n"
++ print("Printing trimming pattern for all reads passing the set threshold values...\n")
+
+ for line in qual:
+ read_number += 1 ### this keeps track of the read order, respected between the prb and seq files
+@@ -156,7 +156,7 @@ def parseQualFile(threshold, difference,
+ if head_match != None:
+ ok_read += 1
+ col = head_match.span()
+- if not trim_info.has_key(read_number):
++ if read_number not in trim_info:
+ trim_info[read_number] = {}
+
+ start = int(col[0])
+@@ -167,7 +167,7 @@ def parseQualFile(threshold, difference,
+
+ if verbose:
+ sub = concat[trim_info[read_number]['start']:trim_info[read_number]['end']]
+- print "passed seqs:%i line#%i %s (start trim:%i,length:%i) %s\n" % (ok_read, read_number, concat, start, end, sub)
++ print("passed seqs:%i line#%i %s (start trim:%i,length:%i) %s\n" % (ok_read, read_number, concat, start, end, sub))
+
+ LOG.write("%i out of %i sequences passed your filter (I >= %i and D >= %i and L >= %i)\n" % (ok_read, read_number, threshold, difference, consecutive))
+
+@@ -191,7 +191,7 @@ def readNTrim(trim_info, seq, verbose, F
+ gDNAlinker2_field = re.compile('^ATCTAACAG')
+
+ if verbose:
+- print "Printing trimmed sequences for all reads passing the set threshold values minus, excluding sequence containing linkers...\n"
++ print("Printing trimmed sequences for all reads passing the set threshold values minus, excluding sequence containing linkers...\n")
+
+ for line in seq:
+ read_number += 1 ### tracks read number / will match order in prb file
+@@ -199,7 +199,7 @@ def readNTrim(trim_info, seq, verbose, F
+ info = line.split("\t") ### split line, the seq file lists: lane tile xcoord y coord DNAseq
+ dna_string = info[4]
+
+- if trim_info.has_key(read_number):
++ if read_number in trim_info:
+ trim_seq = dna_string[trim_info[read_number]['start']:trim_info[read_number]['end']]
+ if re.match(dna_sequence_field, trim_seq): ### no ambiguous bases?
+ if re.match(gDNAlinker1_field, trim_seq) or re.match(gDNAlinker2_field,trim_seq): ### matches gDNA linker?
+@@ -208,7 +208,7 @@ def readNTrim(trim_info, seq, verbose, F
+ usable_reads += 1
+ FASTA.write(">%s-%s-%s-%s\n%s\n" % (info[0],info[1],info[2],info[3],trim_seq))
+ if verbose:
+- print "line#%i %s (start trim:%i,length:%i) %s" % (read_number,info[4],trim_info[read_number]['start'],trim_info[read_number]['end'],trim_seq)
++ print("line#%i %s (start trim:%i,length:%i) %s" % (read_number,info[4],trim_info[read_number]['start'],trim_info[read_number]['end'],trim_seq))
+ LOG.write("%i out of %i sequences appear to be usable, after filtering out sequences hard-coded in this program * %i gDNA linker sequences*\n" % (usable_reads, read_number,gDNAlinker_count))
+ return
+
+--- a/tools/TQS.readme
++++ b/tools/TQS.readme
+@@ -24,12 +24,12 @@ __version__ = '1.0'
+
+ Execution example
+ ==================
+-python TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20
++python3 TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20
+
+
+ Options
+ =======
+-python TQS.py --help
++python3 TQS.py --help
+
+ Usage: TQS.py [options]
+
+--- a/tools/TQSexport.py
++++ b/tools/TQSexport.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ __doc__ = """
+ TQS
+@@ -47,9 +47,9 @@ def main():
+ f = open(opts.exportfile)
+ seq = f.readlines()
+ f.close()
+- except Exception, e:
+- print "ERROR: Could not read from %s: %s" % (opts.exportfile, e)
+- print usage % (sys.argv[0:])
++ except Exception as e:
++ print("ERROR: Could not read from %s: %s" % (opts.exportfile, e))
++ print(usage % (sys.argv[0:]))
+ sys.exit()
+
+
+@@ -61,17 +61,17 @@ def main():
+ try:
+ FASTA = open(fasta, 'w')
+ except:
+- print "ERROR: Can not write to %s" % fasta
++ print("ERROR: Can not write to %s" % fasta)
+ sys.exit()
+
+ try:
+ LOG = open(log, 'w')
+ except:
+- print "ERROR: Can not write to %s" % log
++ print("ERROR: Can not write to %s" % log)
+ sys.exit()
+
+ if opts.consec < minimum_length:
+- print "ERROR: -c must be a number larger than %i." % (minimum_length)
++ print("ERROR: -c must be a number larger than %i." % (minimum_length))
+ sys.exit()
+
+ LOG.write("""
+@@ -106,7 +106,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr
+ read_number = 0
+
+ if verbose:
+- print "Printing trimming pattern for all reads passing the set threshold values...\n"
++ print("Printing trimming pattern for all reads passing the set threshold values...\n")
+
+ for line in export:
+ read_number += 1
+@@ -134,7 +134,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr
+ if head_match != None:
+ ok_read += 1
+ col = head_match.span()
+- if not trim_info.has_key(read_number):
++ if read_number not in trim_info:
+ trim_info[read_number] = {}
+
+ start = int(col[0])
+@@ -150,7 +150,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr
+ FASTA.write(">%s-%s-%s-%s%s\n%s\n" % (info[1],info[2],info[3],info[4],pair,trim_seq))
+
+ if verbose:
+- print "passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (ok_read, read_number, concat, start, end, trim_seq)
++ print("passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (ok_read, read_number, concat, start, end, trim_seq))
+
+ LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive))
+
+--- a/tools/TQSfastq.py
++++ b/tools/TQSfastq.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ __doc__ = """
+ TQS
+@@ -52,9 +52,9 @@ def main():
+ f = open(opts.fastqfile)
+ seq = f.readlines()
+ f.close()
+- except Exception, e:
+- print "ERROR: Could not read from %s: %s" % (opts.fastqfile, e)
+- print usage % (sys.argv[0:])
++ except Exception as e:
++ print("ERROR: Could not read from %s: %s" % (opts.fastqfile, e))
++ print(usage % (sys.argv[0:]))
+ sys.exit()
+
+
+@@ -66,21 +66,21 @@ def main():
+ try:
+ FASTA = open(fasta, 'w')
+ except:
+- print "ERROR: Can not write to %s" % fasta
++ print("ERROR: Can not write to %s" % fasta)
+ sys.exit()
+
+ try:
+ LOG = open(log, 'w')
+ except:
+- print "ERROR: Can not write to %s" % log
++ print("ERROR: Can not write to %s" % log)
+ sys.exit()
+
+ if opts.consec < minimum_length:
+- print "ERROR: -c must be a number larger than %i." % (minimum_length)
++ print("ERROR: -c must be a number larger than %i." % (minimum_length))
+ sys.exit()
+
+ if opts.encoding != 33 and opts.encoding != 64:
+- print "ERROR: -e must be either 33 or 64."
++ print("ERROR: -e must be either 33 or 64.")
+ sys.exit()
+
+ LOG.write("""
+@@ -115,7 +115,7 @@ def readNtrim(fastq, threshold, consecut
+ record_line = 0
+
+ if verbose:
+- print "Printing trimming pattern for all reads passing the set threshold values...\n"
++ print("Printing trimming pattern for all reads passing the set threshold values...\n")
+
+ for line in fastq:
+ record_line += 1
+@@ -161,7 +161,7 @@ def readNtrim(fastq, threshold, consecut
+ FASTA.write(">%s\n%s\n" % (read_id, trim_seq))
+
+ if verbose:
+- print "%s\n%s\n%s\n passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (read_id,seq,qual,ok_read, read_number, concat, start, end, trim_seq)
++ print("%s\n%s\n%s\n passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (read_id,seq,qual,ok_read, read_number, concat, start, end, trim_seq))
+
+ """LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive))"""
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
do_not_send_mail_after_testing.patch
no_privacy_breach_logo.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -30,12 +30,12 @@ override_dh_installexamples:
override_dh_installdocs:
dh_installdocs
- markdown_py -f $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/README.html readme.md
+ markdown readme.md > $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/README.html
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-TESTDIR := $(shell mktemp -d)
override_dh_auto_test:
- cp -a test/* $(TESTDIR)
- cd $(TESTDIR) && $(CURDIR)/SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -r 0.6 -p 0 -t 0 -c 1 -w 5 -b myFirstSSAKErun
- rm -rf $(TESTDIR)
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ TESTDIR=$$(mktemp -d) ; \
+ cp -a test/* $${TESTDIR} ; \
+ cd $${TESTDIR} && $(CURDIR)/SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -r 0.6 -p 0 -t 0 -c 1 -w 5 -b myFirstSSAKErun
+ rm -rf $${TESTDIR}
endif
=====================================
debian/upstream/metadata
=====================================
@@ -1,24 +1,23 @@
-Name: SSAKE
Reference:
- author: >
- Warren, Rene L. and Sutton, Granger G. and Jones, Steven J. M. and Holt,
- Robert A.
- title: Assembling millions of short DNA sequences using SSAKE
- journal: Bioinformatics
- volume: 23
- number: 4
- pages: 500-501
- doi: 10.1093/bioinformatics/btl629
- PMID: 17158514
- year: 2007
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/4/500
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/4/500.pdf
+ author: >
+ Warren, Rene L. and Sutton, Granger G. and Jones, Steven J. M. and Holt,
+ Robert A.
+ title: Assembling millions of short DNA sequences using SSAKE
+ journal: Bioinformatics
+ volume: 23
+ number: 4
+ pages: 500-501
+ doi: 10.1093/bioinformatics/btl629
+ PMID: 17158514
+ year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/4/500
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/4/500.pdf
Registry:
- - Name: SEQwiki
- Entry: http://seqanswers.com/wiki/SSAKE
- - Name: OMICtools
- Entry: OMICS_00033
- - Name: SciCrunch
- Entry: SCR_010753
- - Name: bio.tools
- Entry: ssake
+- Name: SEQwiki
+ Entry: http://seqanswers.com/wiki/SSAKE
+- Name: OMICtools
+ Entry: OMICS_00033
+- Name: SciCrunch
+ Entry: SCR_010753
+- Name: bio.tools
+ Entry: ssake
View it on GitLab: https://salsa.debian.org/med-team/ssake/compare/34c3e516aa1008f19cfdd93fce92f5e42bc91b80...84fbc90c6c9997aafcc06cdcee96f811a3c0a2b5
--
View it on GitLab: https://salsa.debian.org/med-team/ssake/compare/34c3e516aa1008f19cfdd93fce92f5e42bc91b80...84fbc90c6c9997aafcc06cdcee96f811a3c0a2b5
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