[med-svn] [Git][med-team/python-deeptools][upstream] New upstream version 3.4.3
Steffen Möller
gitlab at salsa.debian.org
Tue May 5 16:37:31 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / python-deeptools
Commits:
90f6c615 by Steffen Moeller at 2020-05-05T17:35:08+02:00
New upstream version 3.4.3
- - - - -
6 changed files:
- CHANGES.txt
- bin/estimateScaleFactor
- 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))
=====================================
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/-/commit/90f6c61587f11e6a4a3e5956286cc48300b34078
--
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/commit/90f6c61587f11e6a4a3e5956286cc48300b34078
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