[med-svn] [Git][med-team/python-deeptools][master] 6 commits: Fixed d/watch
Steffen Möller
gitlab at salsa.debian.org
Wed Apr 8 11:27:00 BST 2020
Steffen Möller pushed to branch master at Debian Med / python-deeptools
Commits:
f93994d2 by Steffen Moeller at 2020-04-08T12:14:46+02:00
Fixed d/watch
In reaction to Ben informing about a problem with updates. Well spotted!
$ ../science-team/routine-update/routine-update clone git at salsa.debian.org:med-team/python-deeptools.git
gbp:info: Cloning from 'git at salsa.debian.org:med-team/python-deeptools.git'
I: Changing into directory 'python-deeptools'
gbp:info: Fetching from default remote for each branch
gbp:info: Branch 'master' is already up to date.
gbp:info: Branch 'upstream' is already up to date.
38c3821f7eaf86df4618d691403335c60d147b28
uscan warn: In debian/watch no matching files for watch line
https://github.com/deeptools/deepTools/releases .*/archive/v(?:[-_]?(\d[\-+\.:\~\da-zA-Z]*))(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
E: Uscan did not return tarball name
- - - - -
57ecb31d by Steffen Moeller at 2020-04-08T12:16:17+02:00
routine-update: New upstream version
- - - - -
7fef8d99 by Steffen Moeller at 2020-04-08T12:16:18+02:00
New upstream version 3.4.2
- - - - -
74f1a23f by Steffen Moeller at 2020-04-08T12:16:36+02:00
Update upstream source from tag 'upstream/3.4.2'
Update to upstream version '3.4.2'
with Debian dir ab7457e746bd0122bff0332379f9b773d7dbfc85
- - - - -
424403fc by Steffen Moeller at 2020-04-08T12:16:43+02:00
Set upstream metadata fields: Repository, Repository-Browse.
- - - - -
06416656 by Steffen Moeller at 2020-04-08T12:17:24+02:00
routine-update: Ready to upload to unstable
- - - - -
15 changed files:
- .github/workflows/test.yml
- CHANGES.txt
- azure-pipelines.yml
- debian/changelog
- debian/upstream/metadata
- debian/watch
- deeptools/_version.py
- deeptools/bamPEFragmentSize.py
- deeptools/correlation.py
- deeptools/parserCommon.py
- deeptools/plotHeatmap.py
- deeptools/writeBedGraph_bam_and_bw.py
- galaxy/wrapper/deepTools_macros.xml
- galaxy/wrapper/plotCoverage.xml
- galaxy/wrapper/plotHeatmap.xml
Changes:
=====================================
.github/workflows/test.yml
=====================================
@@ -32,6 +32,7 @@ jobs:
- uses: "dpryan79/github-actions/@master"
- name: Test deepTools
run: |
+
source activate foo
nosetests --with-doctest -sv deeptools
planemo:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,17 @@
+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
+
+3.4.1
+
+ * Prevented temporary bedGraph files from being written to (possibly small) shared-memory drives even when TMPDIR is set to somewhere else. Now shared memory is only used if requested by setting TMPDIR (or other appropriate environment variables) to `/dev/shm`.
+ * Fixed a bug in bamPEFragmentSize that caused incompatibility with newer matplotlib releases. (issue #928)
+
+3.4.0
+
+ * Fixed a bug in one of the Galaxy wrappers.
+ * Added the `--lineAtTickMarks` option to `plotHeatmap` so that there are dashed vertical lines for each tick mark in the plot. (issue #924)
+
3.3.2
* Fixed --yAxisLabel in plotProfile (issue #889)
=====================================
azure-pipelines.yml
=====================================
@@ -17,19 +17,20 @@ jobs:
displayName: Add conda to PATH
- template: .azure-pipelines/test-template.yml
-- job: 'OSX'
- pool:
- vmImage: 'macOS-10.13'
- strategy:
- matrix:
- Python37:
- python.version: '3.7'
- maxParallel: 1
-
- steps:
- - bash: echo "##vso[task.prependpath]$CONDA/bin"
- displayName: Add conda to PATH
- - template: .azure-pipelines/test-template.yml
+#Fails frequently due to CI issues
+#- job: 'OSX'
+# pool:
+# vmImage: 'macOS-10.14'
+# strategy:
+# matrix:
+# Python37:
+# python.version: '3.7'
+# maxParallel: 1
+#
+# steps:
+# - bash: echo "##vso[task.prependpath]$CONDA/bin"
+# displayName: Add conda to PATH
+# - template: .azure-pipelines/test-template.yml
- job: 'galaxy'
dependsOn: 'Linux'
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-deeptools (3.4.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * Set upstream metadata fields: Repository, Repository-Browse.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 08 Apr 2020 12:16:44 +0200
+
python-deeptools (3.3.2+ds-3) unstable; urgency=medium
[ Sao I Kuan ]
=====================================
debian/upstream/metadata
=====================================
@@ -37,3 +37,5 @@ Registry:
Entry: deeptools
Bug-Database: https://github.com/deeptools/deepTools/issues
Bug-Submit: https://github.com/deeptools/deepTools/issues/new
+Repository: https://github.com/deeptools/deepTools.git
+Repository-Browse: https://github.com/deeptools/deepTools
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
-opts="uversionmangle=s/$/+ds/,dversionmangle=auto,compression=xz,repack" \
- https://github.com/deeptools/deepTools/releases .*/archive/v at ANY_VERSION@@ARCHIVE_EXT@
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-deeptools-$1.tar.gz%" \
+ https://github.com/deeptools/deepTools/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
=====================================
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__ = '3.3.2'
+__version__ = '3.4.2'
=====================================
deeptools/bamPEFragmentSize.py
=====================================
@@ -119,7 +119,7 @@ def getDensity(lengths, minVal, maxVal):
This is essentially computing what hist() in matplotlib is doing and returning the results.
This then allows us to free up the memory consumed by each sample rather than returning it all back to main() for plotting.
"""
- n, bins, patches = plt.hist(lengths, bins=100, range=(minVal, maxVal), normed=True)
+ n, bins, patches = plt.hist(lengths, bins=100, range=(minVal, maxVal), density=True)
plt.clf()
return (n, bins)
=====================================
deeptools/correlation.py
=====================================
@@ -527,9 +527,9 @@ class Correlation:
else:
ax.set_xticklabels([])
- ax.hist2d(vector2, vector1, bins=200, cmin=0.1)
ax.set_xlim(min_xvalue, max_xvalue)
ax.set_ylim(min_yvalue, max_yvalue)
+ ax.hist2d(vector2, vector1, bins=200, cmin=0.1)
plt.savefig(plot_filename, format=image_format)
plt.close()
=====================================
deeptools/parserCommon.py
=====================================
@@ -611,6 +611,12 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
'example: --sortUsingSamples 1 3',
type=int, nargs='+')
+ optional.add_argument('--linesAtTickMarks',
+ help='Draw dashed lines from all tick marks through the heatmap. '
+ 'This is then similar to the dashed line draw at region bounds '
+ 'when using a reference point and --sortUsing region_length',
+ action='store_true')
+
optional.add_argument('--clusterUsingSamples',
help='List of sample numbers (order as in '
'matrix), that are used for clustering by '
=====================================
deeptools/plotHeatmap.py
=====================================
@@ -389,6 +389,7 @@ def plotMatrix(hm, outFileName,
heatmapWidth=7.5,
perGroup=False, whatToShow='plot, heatmap and colorbar',
plot_type='lines',
+ linesAtTickMarks=False,
image_format=None,
legend_location='upper-left',
box_around_heatmaps=True,
@@ -539,7 +540,7 @@ def plotMatrix(hm, outFileName,
_len *= 0.5
_reg_len.append((hm.parameters['upstream'][idx] + _len) / hm.parameters['bin size'][idx])
elif hm.parameters['ref point'][idx] == 'TES':
- _reg_len.append((hm.parameters['downstream'][idx] - _len) / hm.parameters['bin size'][idx])
+ _reg_len.append((hm.parameters['upstream'][idx] - _len) / hm.parameters['bin size'][idx])
foo.append(_reg_len)
regions_length_in_bins[idx] = foo
@@ -659,6 +660,18 @@ def plotMatrix(hm, outFileName,
elif not perGroup and sample == 0:
ax.axes.set_ylabel(sub_matrix['group'])
+ # Plot vertical lines at tick marks if desired
+ if linesAtTickMarks:
+ xticks_heat, xtickslabel_heat = hm.getTicks(sample)
+ xticks_heat = [x + 0.5 for x in xticks_heat] # There's an offset of 0.5 compared to the profile plot
+ if np.ceil(max(xticks_heat)) != float(sub_matrix['matrix'].shape[1]):
+ tickscale = float(sub_matrix['matrix'].shape[1]) / max(xticks_heat)
+ xticks_heat_use = [x * tickscale for x in xticks_heat]
+ else:
+ xticks_heat_use = xticks_heat
+ for x in xticks_heat_use:
+ ax.axvline(x=x, color='black', linewidth=0.5, dashes=(3, 2))
+
# add labels to last block in a column
if (perGroup and sample == numsamples - 1) or \
(not perGroup and group_idx == numgroups - 1):
@@ -845,6 +858,7 @@ def main(args=None):
args.heatmapWidth,
args.perGroup,
args.whatToShow,
+ linesAtTickMarks=args.linesAtTickMarks,
plot_type=args.plotType,
image_format=args.plotFileFormat,
legend_location=args.legendLocation,
=====================================
deeptools/writeBedGraph_bam_and_bw.py
=====================================
@@ -76,12 +76,7 @@ def writeBedGraph_worker(
tileSize, missingDataAsZero))
bigwigHandle.close()
- # is /dev/shm available?
- # working in this directory speeds the process
- try:
- _file = tempfile.NamedTemporaryFile(dir="/dev/shm", delete=False)
- except OSError:
- _file = tempfile.NamedTemporaryFile(delete=False)
+ _file = tempfile.NamedTemporaryFile(delete=False)
previousValue = None
lengthCoverage = len(coverage[0])
=====================================
galaxy/wrapper/deepTools_macros.xml
=====================================
@@ -1,10 +1,10 @@
<macros>
<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
- <token name="@WRAPPER_VERSION@">3.3.2.0</token>
+ <token name="@WRAPPER_VERSION@">3.4.2.0</token>
<xml name="requirements">
<requirements>
- <requirement type="package" version="3.3.2">deeptools</requirement>
+ <requirement type="package" version="3.4.2">deeptools</requirement>
<requirement type="package" version="1.9">samtools</requirement>
</requirements>
<expand macro="stdio" />
=====================================
galaxy/wrapper/plotCoverage.xml
=====================================
@@ -26,7 +26,7 @@
#end if
#if ' '.join(map(str, $BED)) != 'None':
- #set bedFileLList=[]
+ #set bedFileList=[]
#for $f in $BED:
#silent $bedFileList.append("'%s'" % $f)
#end for
@@ -101,11 +101,8 @@
<expand macro="blacklist" />
</when>
</conditional>
-
<expand macro="input_image_file_format" />
<param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
-
-
</inputs>
<outputs>
<expand macro="output_image_file_format_not_nested" />
=====================================
galaxy/wrapper/plotHeatmap.xml
=====================================
@@ -34,6 +34,10 @@
--sortRegions '$advancedOpt.sortRegions'
#end if
+ #if $advancedOpt.linesAtTickMarks:
+ --linesAtTickMarks
+ #end if
+
#if $advancedOpt.sortUsing:
--sortUsing '$advancedOpt.sortUsing'
#end if
@@ -130,6 +134,8 @@
<when value="yes">
<expand macro="sortRegions" />
<expand macro="sortUsing" />
+ <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
+ label="Draw dashed lines in heatmap above all tick marks?" />
<param argument="--averageTypeSummaryPlot" type="select"
label="Type of statistic that should be plotted in the summary image above the heatmap"
help="">
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/38c3821f7eaf86df4618d691403335c60d147b28...064166562018c795f7d3e73b498588729cae03ac
--
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/38c3821f7eaf86df4618d691403335c60d147b28...064166562018c795f7d3e73b498588729cae03ac
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200408/38a460f6/attachment-0001.html>
More information about the debian-med-commit
mailing list