[med-svn] [Git][med-team/sga][debian/unstable] 9 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Mon Sep 2 19:51:21 BST 2019
Andreas Tille pushed to branch debian/unstable at Debian Med / sga
Commits:
1db00556 by Andreas Tille at 2019-09-02T18:20:15Z
Use 2to3 to port to Python3
- - - - -
51d61e2d by Andreas Tille at 2019-09-02T18:21:00Z
Adjust (Build-)Depends
- - - - -
0d89879e by Andreas Tille at 2019-09-02T18:21:23Z
debhelper-compat 12
- - - - -
2b4b5b8b by Andreas Tille at 2019-09-02T18:21:26Z
Standards-Version: 4.4.0
- - - - -
db1be50f by Andreas Tille at 2019-09-02T18:21:27Z
Secure URI in copyright format
- - - - -
9f9ad8bd by Andreas Tille at 2019-09-02T18:21:27Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
b9723af4 by Andreas Tille at 2019-09-02T18:21:29Z
Set fields Upstream-Contact in debian/copyright.
- - - - -
79cdf7b8 by Andreas Tille at 2019-09-02T18:21:30Z
Remove obsolete fields Name, Contact from debian/upstream/metadata.
- - - - -
424abe8d by Andreas Tille at 2019-09-02T18:41:23Z
s/python/python3/
- - - - -
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 +1,16 @@
+sga (0.10.15-5) UNRELEASED; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: 938472
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Secure URI in copyright format
+ * Trim trailing whitespace.
+ * Set fields Upstream-Contact in debian/copyright.
+ * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Mon, 02 Sep 2019 20:18:33 +0200
+
sga (0.10.15-4) unstable; urgency=medium
* debhelper 11
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
libsparsehash-dev,
zlib1g-dev | libz-dev,
libbamtools-dev,
@@ -13,10 +13,10 @@ Build-Depends: debhelper (>= 11~),
# Run-Time Depends
# (to prevent building on architectures where it won't be installable)
samtools,
- python,
- python-ruffus,
- python-pysam
-Standards-Version: 4.2.1
+ python3,
+ python3-ruffus,
+ python3-pysam
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/sga
Vcs-Git: https://salsa.debian.org/med-team/sga.git
Homepage: https://github.com/jts/sga
@@ -26,9 +26,9 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
samtools,
- python,
- python-ruffus,
- python-pysam
+ python3,
+ python3-ruffus,
+ python3-pysam
Recommends: abyss (>= 2.0.2-1)
Description: de novo genome assembler that uses string graphs
The major goal of SGA is to be very memory efficient, which is achieved by
=====================================
debian/copyright
=====================================
@@ -1,6 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: sga
Source: https://github.com/jts/sga
+Upstream-Contact: http://groups.google.com/group/sga-users
Files: *
Copyright: 2009-2012 Jared T. Simpson <js18 at sanger.ac.uk>
@@ -87,4 +88,3 @@ License: Expat
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,95 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/938472
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 02 Sep 2019 20:18:33 +0200
+
+
+--- a/src/bin/sga-astat.py
++++ b/src/bin/sga-astat.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ #
+ # sga-astat.py - Compute Myers' a-statistic for a set of contigs using read alignments
+ # in a bam file
+@@ -30,20 +30,20 @@ genomeSize = 0
+ arrivalRate = 0
+
+ def usage():
+- print 'usage: sga-astat.py in.bam'
+- print 'Compute Myers\' a-statistic for a set of contigs using the read alignments in in.bam'
+- print 'Options:'
+- print ' -m=INT only compute a-stat for contigs at least INT bases in length'
+- print ' -b=INT use the longest INT contigs to perform the initial estimate'
+- print ' of the arrival rate (default: ' + str(numContigsForInitialEstimate) + ')'
+- print ' -n=INT perform INT bootstrap iterations of the estimate'
+- print ' -g=INT use INT as the genome size instead of estimating it'
+- print ' --no-duplicates do not use duplicate reads to calculate statistics'
++ print('usage: sga-astat.py in.bam')
++ print('Compute Myers\' a-statistic for a set of contigs using the read alignments in in.bam')
++ print('Options:')
++ print(' -m=INT only compute a-stat for contigs at least INT bases in length')
++ print(' -b=INT use the longest INT contigs to perform the initial estimate')
++ print(' of the arrival rate (default: ' + str(numContigsForInitialEstimate) + ')')
++ print(' -n=INT perform INT bootstrap iterations of the estimate')
++ print(' -g=INT use INT as the genome size instead of estimating it')
++ print(' --no-duplicates do not use duplicate reads to calculate statistics')
+
+ try:
+ opts, args = getopt.gnu_getopt(sys.argv[1:], 'm:b:n:g:', ['help', 'no-duplicates'])
+-except getopt.GetoptError, err:
+- print str(err)
++except getopt.GetoptError as err:
++ print(str(err))
+ usage()
+ sys.exit(2)
+
+@@ -63,7 +63,7 @@ for (oflag, oarg) in opts:
+ sys.exit(1)
+
+ if len(args) == 0:
+- print 'Error: a BAM file must be provided\n'
++ print('Error: a BAM file must be provided\n')
+ usage()
+ sys.exit(2)
+
+@@ -172,7 +172,7 @@ sumUnique = 0
+ sumRepeat = 0
+ for cd in contigData:
+ if cd.len >= minLength and cd.nlen > 0:
+- print '%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat)
++ print('%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat))
+
+ if cd.bUnique:
+ sumUnique += cd.len
+--- a/src/bin/sga-preqc-report.py
++++ b/src/bin/sga-preqc-report.py
+@@ -1,8 +1,8 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Generate a readable report from preqc output.
+ """
+
+-from __future__ import print_function, division
++
+
+ import sys, os.path
+ import matplotlib as MPL
+@@ -458,7 +458,7 @@ def plot_mean_quality_scores(ax, data, l
+ 'mean_quality' in d[QUALITY_SCORE_NAME] ):
+ names.append(d['name'])
+ mean_quality = d[QUALITY_SCORE_NAME]['mean_quality']
+- indices = range(0, len(mean_quality))
++ indices = list(range(0, len(mean_quality)))
+ marker = d['plot_marker'] if( use_markers ) else None
+ ax.plot(indices, mean_quality, '-',
+ marker=marker, color=d['plot_color'])
+@@ -478,7 +478,7 @@ def plot_q30_quality_scores(ax, data, le
+ 'fraction_q30' in d[QUALITY_SCORE_NAME] ):
+ names.append(d['name'])
+ q30_fraction = d[QUALITY_SCORE_NAME]['fraction_q30']
+- indices = range(0, len(q30_fraction))
++ indices = list(range(0, len(q30_fraction)))
+ marker = d['plot_marker'] if( use_markers ) else None
+ ax.plot(indices, q30_fraction, '-',
+ marker=marker, color=d['plot_color'])
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@
0006-remove-google-addsense.patch
gcc-7.patch
no_privacy_breach_url.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -53,4 +53,3 @@ override_dh_installman:
--name="generate sga merge commands from a list of files" \
--output $(mandir)/sga-mergeDriver.1 \
$(bindir)/sga-mergeDriver
-
=====================================
debian/upstream/metadata
=====================================
@@ -1,27 +1,25 @@
-Contact: http://groups.google.com/group/sga-users
FAQ: https://github.com/jts/sga/wiki/FAQ
-Name: SGA (String Graph Assembler)
Reference:
- Author: Jared T. Simpson and Richard Durbin
- DOI: 10.1101/gr.126953.111
- Eprint: http://genome.cshlp.org/content/22/3/549.full.pdf
- Journal: Genome Res
- Number: 3
- Pages: 549-555
- PMID: 22156294
- Title: Efficient de novo assembly of large genomes using compressed data structures.
- Type: article
- URL: http://genome.cshlp.org/content/22/3/549.abstract
- Volume: 22
- Year: 2012
+ Author: Jared T. Simpson and Richard Durbin
+ DOI: 10.1101/gr.126953.111
+ Eprint: http://genome.cshlp.org/content/22/3/549.full.pdf
+ Journal: Genome Res
+ Number: 3
+ Pages: 549-555
+ PMID: 22156294
+ Title: Efficient de novo assembly of large genomes using compressed data structures.
+ Type: article
+ URL: http://genome.cshlp.org/content/22/3/549.abstract
+ Volume: 22
+ Year: 2012
Repository: git://github.com/jts/sga.git
Repository-Browse: https://github.com/jts/sga/tree/master/src
Bug-Database: https://github.com/jts/sga/issues
Bug-Submit: https://github.com/jts/sga/issues/new
Registry:
- - Name: OMICtools
- Entry: OMICS_00028
- - Name: bio.tools
- Entry: SGA
- - Name: SciCrunch
- Entry: SCR_001982
+- Name: OMICtools
+ Entry: OMICS_00028
+- Name: bio.tools
+ Entry: SGA
+- Name: SciCrunch
+ Entry: SCR_001982
View it on GitLab: https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63
--
View it on GitLab: https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63
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