Steffen Möller pushed to branch master at Debian Med / python-deeptools
Commits: 80bc61c7 by Steffen Moeller at 2020-05-05T17:35:07+02:00 routine-update: New upstream version - - - - - 90f6c615 by Steffen Moeller at 2020-05-05T17:35:08+02:00 New upstream version 3.4.3 - - - - - daefa66b by Steffen Moeller at 2020-05-05T17:35:24+02:00 Update upstream source from tag 'upstream/3.4.3' Update to upstream version '3.4.3' with Debian dir 3d39b53ee0d65031e66a76342cbae421cc9f6c32 - - - - - 911dd5dc by Steffen Moeller at 2020-05-05T17:36:07+02:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - CHANGES.txt - bin/estimateScaleFactor - debian/changelog - deeptools/_version.py - deeptools/parserCommon.py - deeptools/plotProfile.py - galaxy/wrapper/deepTools_macros.xml Changes: ===================================== CHANGES.txt ===================================== @@ -1,3 +1,8 @@ +3.4.3 + + * Changed iteritems() in estimateEscaleFactor to its python3 compatible items(). + * Added the missing argument (--clusterUsingSamples) to plotProfile. + 3.4.2 * Programmed around a bug in matplotlib that prevented the plotCorrelation scatter plot from working. See https://bioinformatics.stackexchange.com/questions/12830/plot-correlation-between-several-bam-files/12831 @@ -325,7 +330,7 @@ * bamPEFragmentSize now has -bs and -n options to allow adjusting the number of alignments sampled. Note that the default value is auto-adjusted if the sampling is too sparse. * bamPEFragmentSize now accepts single-end files. * The --hclust option to plotProfile and plotHeatmap continues even if one of the groups is too small for plotting (matplotlib will produce a warning that you can ignore). This was issue #280. - + 2.0.1 * A critical bug that prevented plotPCA from running was fixed. ===================================== bin/estimateScaleFactor ===================================== @@ -89,9 +89,9 @@ def parseArguments(args=None): def main(args): """ - The algorithm samples the genome a number of times as specified + The algorithm samples the genome a number of times as specified by the --numberOfSamples parameter to estimate scaling factors of - betweeen to samples + betweeen to samples """ if len(args.bamfiles) > 2: @@ -99,14 +99,14 @@ def main(args): exit(0) sys.stderr.write("{:,} number of samples will be computed.\n".format(args.numberOfSamples)) - sizeFactorsDict = estimateScaleFactor(args.bamfiles, args.sampleWindowLength, + sizeFactorsDict = estimateScaleFactor(args.bamfiles, args.sampleWindowLength, args.numberOfSamples, args.normalizationLength, numberOfProcessors=args.numberOfProcessors, chrsToSkip=args.ignoreForNormalization, verbose=args.verbose) - for k, v in sizeFactorsDict.iteritems(): + for k, v in sizeFactorsDict.items(): print("{}: {}".format(k, v)) ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +python-deeptools (3.4.3-1) unstable; urgency=medium + + * New upstream version + + -- Steffen Moeller <[email protected]> Tue, 05 May 2020 17:35:30 +0200 + python-deeptools (3.4.2-1) unstable; urgency=medium * New upstream version ===================================== deeptools/_version.py ===================================== @@ -2,4 +2,4 @@ # This file is originally generated from Git information by running 'setup.py # version'. Distribution tarballs contain a pre-generated copy of this file. -__version__ = '3.4.2' +__version__ = '3.4.3' ===================================== deeptools/parserCommon.py ===================================== @@ -573,6 +573,14 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]): type=int, default=8) + optional.add_argument('--clusterUsingSamples', + help='List of sample numbers (order as in ' + 'matrix), that are used for clustering by ' + '--kmeans or --hclust if not given, all samples ' + 'are taken into account for clustering. ' + 'Example: --ClusterUsingSamples 1 3', + type=int, nargs='+') + elif mode == 'heatmap': optional.add_argument( '--plotType', ===================================== deeptools/plotProfile.py ===================================== @@ -909,12 +909,12 @@ def main(args=None): filterHeatmapValues(hm, hm.parameters['min threshold'], hm.parameters['max threshold']) if args.kmeans is not None: - hm.matrix.hmcluster(args.kmeans, method='kmeans') + hm.matrix.hmcluster(args.kmeans, method='kmeans', clustering_samples=args.clusterUsingSamples) else: if args.hclust is not None: print("Performing hierarchical clustering." "Please note that it might be very slow for large datasets.\n") - hm.matrix.hmcluster(args.hclust, method='hierarchical') + hm.matrix.hmcluster(args.hclust, method='hierarchical', clustering_samples=args.clusterUsingSamples) group_len_ratio = np.diff(hm.matrix.group_boundaries) / float(len(hm.matrix.regions)) if np.any(group_len_ratio < 5.0 / 1000): ===================================== galaxy/wrapper/deepTools_macros.xml ===================================== @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.4.2.0</token> + <token name="@WRAPPER_VERSION@">3.4.3.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.4.2">deeptools</requirement> + <requirement type="package" version="3.4.3">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" /> View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc -- View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc You're receiving this email because of your account on salsa.debian.org.
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