Andreas Tille pushed to branch master at Debian Med / tiddit
Commits: 5573c455 by Andreas Tille at 2020-06-16T22:08:50+02:00 New upstream version 2.12.0+dfsg - - - - - 896a7e4a by Andreas Tille at 2020-06-16T22:08:50+02:00 routine-update: New upstream version - - - - - 046921cc by Andreas Tille at 2020-06-16T22:08:50+02:00 Update upstream source from tag 'upstream/2.12.0+dfsg' Update to upstream version '2.12.0+dfsg' with Debian dir 7233100093e735edf5ac12edfbf1a0a5dcdcb67e - - - - - 0ceaa361 by Andreas Tille at 2020-06-16T22:08:51+02:00 routine-update: debhelper-compat 13 - - - - - 1dcbe52e by Andreas Tille at 2020-06-16T22:08:54+02:00 routine-update: Rules-Requires-Root: no - - - - - 9882d404 by Andreas Tille at 2020-06-16T22:08:57+02:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - 8418e325 by Andreas Tille at 2020-06-16T22:10:03+02:00 routine-update: Ready to upload to unstable - - - - - 8 changed files: - TIDDIT.py - debian/changelog - debian/control - debian/upstream/metadata - src/TIDDIT.cpp - src/TIDDIT_calling.py - src/TIDDIT_coverage.py - + versioned_singularity/TIDDIT.2.12.0 Changes: ===================================== TIDDIT.py ===================================== @@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__)) sys.path.insert(0, '{}/src/'.format(wd)) import TIDDIT_calling -version = "2.11.0" +version = "2.12.0" parser = argparse.ArgumentParser("""TIDDIT-{}""".format(version),add_help=False) parser.add_argument('--sv' , help="call structural variation", required=False, action="store_true") parser.add_argument('--cov' , help="generate a coverage bed file", required=False, action="store_true") ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +tiddit (2.12.0+dfsg-1) unstable; urgency=medium + + * New upstream version + * debhelper-compat 13 (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. + + -- Andreas Tille <[email protected]> Tue, 16 Jun 2020 22:08:57 +0200 + tiddit (2.11.0+dfsg-1) unstable; urgency=medium * Initial release (Closes: #961659) ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), cmake, dh-python, cython3, @@ -14,6 +14,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tiddit Vcs-Git: https://salsa.debian.org/med-team/tiddit.git Homepage: https://github.com/SciLifeLab/TIDDIT +Rules-Requires-Root: no Package: tiddit Architecture: any ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,7 @@ +Bug-Database: https://github.com/SciLifeLab/TIDDIT/issues +Bug-Submit: https://github.com/SciLifeLab/TIDDIT/issues/new Registry: - Name: conda:bioconda Entry: tiddit +Repository: https://github.com/SciLifeLab/TIDDIT.git +Repository-Browse: https://github.com/SciLifeLab/TIDDIT ===================================== src/TIDDIT.cpp ===================================== @@ -46,7 +46,7 @@ int main(int argc, char **argv) { int min_variant_size= 100; int sample = 100000000; string outputFileHeader ="output"; - string version = "2.11.0"; + string version = "2.12.0"; //collect all options as a vector vector<string> arguments(argv, argv + argc); ===================================== src/TIDDIT_calling.py ===================================== @@ -234,9 +234,21 @@ def cluster(args): for chrA in chromosomes: calls[chrA] =[] print ("{}".format(chrA)) + signals_chrA={} + signals=[ [hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7],hit[8]] for hit in args.c.execute('SELECT chrB,posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == \'{}\''.format(chrA)).fetchall()] + for chrB in chromosomes: - signal_data=numpy.array([ [hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7]] for hit in args.c.execute('SELECT posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == \'{}\' AND chrB == \'{}\''.format(chrA,chrB)).fetchall()]) + if not chrB in signals_chrA: + signals_chrA[chrB] = [] + + for signal in signals: + signals_chrA[signal[0]].append(signal[1:]) + for chrB in signals_chrA: + signals_chrA[chrB]=numpy.array(signals_chrA[chrB]) + + for chrB in chromosomes: + signal_data=signals_chrA[chrB] if not len(signal_data): continue ===================================== src/TIDDIT_coverage.py ===================================== @@ -88,7 +88,7 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats): print ("make sure that the contigs of the bam file and the reference match") quit() - if len(cov): + if cov.size: coverage_norm=numpy.median(cov) else: coverage_norm=1 @@ -107,7 +107,11 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats): else: cov=coverage_data[chromosome][numpy.where( (coverage_data[chromosome][:,1] > args.Q) | (coverage_data[chromosome][:,1] == 0) ),0] - chromosomal_average=numpy.median(cov) + if cov.size: + chromosomal_average=numpy.median(cov) + else: + chromosomal_average=0 + if not args.force_ploidy: try: ploidies[chromosome]=int(round((chromosomal_average)/coverage_norm*args.n)) ===================================== versioned_singularity/TIDDIT.2.12.0 ===================================== @@ -0,0 +1,23 @@ +BootStrap: debootstrap +OSVersion: trusty +MirrorURL: http://us.archive.ubuntu.com/ubuntu/ + + +%runscript + echo "This is what happens when you run the container..." + + +%post + echo "Hello from inside the container" + sed -i 's/$/ universe/' /etc/apt/sources.list + apt-get update + apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip + easy_install pip + pip install numpy cython + + wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.0.zip + unzip TIDDIT-2.12.0.zip + + mv TIDDIT-TIDDIT-2.12.0/* /bin/ + cd /bin/ && ./INSTALL.sh + chmod +x /bin/TIDDIT.py View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1 -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1 You're receiving this email because of your account on salsa.debian.org.
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