.azure-pipelines/test-template.yml

 steps:
-- bash: conda create -n foo -q --yes -c conda-forge -c bioconda numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython
+- bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals
   displayName: Installing dependencies
 - bash: |
     source activate foo
-    python setup.py install
+    python -m pip install . --no-deps --ignore-installed -vvv
   displayName: Installing deeptools
 - bash: |
     source activate foo

.github/workflows/pypi.yml

+name: pypi
+on: [push]
+jobs:
+  pypi:
+    name: upload to pypi
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup conda
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+    - name: create env
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine
+    - name: sdist
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        rm -f dist/*
+        python setup.py sdist
+    - name: upload
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      env:
+        TWINE_USERNAME: "__token__"
+        TWINE_PASSWORD: ${{ secrets.pypi_password }}
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        twine upload dist/*

.github/workflows/test.yml

+name: Test
+on: [push]
+jobs:
+  build-linux:
+    name: Test on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup conda
+      run: |
+        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+    - name: create env
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals
+    - name: install deeptools
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        python -m pip install . --no-deps --ignore-installed -vvv
+    - name: PEP8
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605
+    - name: Test deepTools
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        nosetests --with-doctest -sv deeptools
+  build-osx:
+    name: Test on OSX
+    runs-on: macOS-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup conda
+      run: |
+        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+    - name: create env
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals
+    - name: install deeptools
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        python -m pip install . --no-deps --ignore-installed -vvv
+    - name: Test deepTools
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        nosetests --with-doctest -sv deeptools
+  planemo:
+    name: First planemo chunk
+    runs-on: ubuntu-latest
+    needs: build-linux
+    strategy:
+      matrix:
+        chunk: [1, 2, 3]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup conda
+      run: |
+        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+    - name: create env
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals planemo samtools
+    - name: install deeptools
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        python -m pip install . --no-deps --ignore-installed -vvv
+    - name: planemo
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        ./.planemo.sh ${{ matrix.chunk }}

CHANGES.txt

+3.3.1
+
+ * Fixed `--plotNumbers` not working in `plotCorrelation`. This was issue #838.
+ * Fixed compatibility with matplotlib 3 and restrict to at least that version.
+ * The Y-axis labels should once again appear in both plotHeatmap and plotProfile (issue #844). This was related to the previous point.
+ * Testing is no longer performed with python 2.7, which will reach end of life in a couple months.
+ * Various documentation updates (issues #868, #867 and #851).
+ * Increased support for BED files with track header lines (issue #866).
+
 3.3.0
 
  * `plotCoverage` now has a `--BED` option, to restrict plots and output to apply to a specific set of regions given by a BED or GTF file or files (issue #829).

azure-pipelines.yml

@@ -8,8 +8,6 @@ jobs:
     vmImage: 'ubuntu-16.04'
   strategy:
     matrix:
-      Python27:
-        python.version: '2.7'
       Python37:
         python.version: '3.7'
     maxParallel: 4
@@ -24,8 +22,6 @@ jobs:
     vmImage: 'macOS-10.13'
   strategy:
     matrix:
-      Python27:
-        python.version: '2.7'
       Python37:
         python.version: '3.7'
     maxParallel: 1
@@ -54,7 +50,7 @@ jobs:
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
     displayName: Add conda to PATH
-  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython planemo setuptools
+  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals planemo samtools
     displayName: Installing dependencies
   - bash: |
       source activate foo

debian/changelog

-python-deeptools (3.3.0-1) UNSTABLE; urgency=medium
+python-deeptools (3.3.1-1) UNSTABLE; urgency=medium
 
   * Initial release (Closes: #934321)
 
+ -- Steffen Moeller <moeller@debian.org>  Thu, 26 Sep 2019 14:37:35 +0200
+
+python-deeptools (3.3.0-1) UNSTABLE; urgency=medium
+
+  * Initial packaging
+
     TODO: build documentation, would involve fixing/overriding this
           lintian error:
            source-is-missing docs/_static/welcome_owl.carousel.min.js

debian/patches/deactivateFailingPatch.patch

-Index: python-deeptools/deeptools/test/testskip_heatmapper_images.py
-===================================================================
---- python-deeptools.orig/deeptools/test/testskip_heatmapper_images.py
-+++ python-deeptools/deeptools/test/testskip_heatmapper_images.py
-@@ -69,14 +69,14 @@ def test_plotHeatmap_multiple_colors_mut
-     os.remove(outfile.name)
- 
- 
--def test_plotHeatmap_multiple_colormap_no_boxes():
--    outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
--    args = "-m {}/master_multi.mat.gz --colorMap Reds binary terrain --boxAroundHeatmaps no " \
--           "--outFileName {}".format(ROOT, outfile.name).split()
--    deeptools.plotHeatmap.main(args)
--    res = compare_images(ROOT + '/heatmap_master_multi_colormap_no_box.png', outfile.name, tolerance)
--    assert res is None, res
--    os.remove(outfile.name)
-+#def test_plotHeatmap_multiple_colormap_no_boxes():
-+#    outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
-+#    args = "-m {}/master_multi.mat.gz --colorMap Reds binary terrain --boxAroundHeatmaps no " \
-+#           "--outFileName {}".format(ROOT, outfile.name).split()
-+#    deeptools.plotHeatmap.main(args)
-+#    res = compare_images(ROOT + '/heatmap_master_multi_colormap_no_box.png', outfile.name, tolerance)
-+#    assert res is None, res
-+#    os.remove(outfile.name)
- 
- 
- def test_plotHeatmap_interpolation():

debian/patches/series

 python2to3_for_executables.patch
-deactivateFailingPatch.patch

debian/upstream/metadata

@@ -33,4 +33,5 @@ Registry:
    Entry: OMICS_08441
  - Name: bio.tools
    Entry: deeptools
-   
+ - Name: conda:bioconda
+   Entry: deeptools  

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__ = '3.3.0'
+__version__ = '3.3.1'

deeptools/alignmentSieve.py

@@ -30,7 +30,7 @@ def parseArguments():
     general.add_argument('--numberOfProcessors', '-p',
                          help='Number of processors to use. Type "max/2" to '
                          'use half the maximum number of processors or "max" '
-                         'to use all available processors.',
+                         'to use all available processors. (Default: %(default)s)',
                          metavar="INT",
                          type=parserCommon.numberOfProcessors,
                          default=1,
@@ -80,7 +80,7 @@ def parseArguments():
 
     filtering.add_argument('--filterRNAstrand',
                            help='Selects RNA-seq reads (single-end or paired-end) in '
-                                'the given strand.',
+                                'the given strand. (Default: %(default)s)',
                            choices=['forward', 'reverse'],
                            default=None)
 
@@ -129,7 +129,7 @@ def parseArguments():
                            help='The minimum fragment length needed for read/pair '
                            'inclusion. This option is primarily useful '
                            'in ATACseq experiments, for filtering mono- or '
-                           'di-nucleosome fragments.',
+                           'di-nucleosome fragments. (Default: %(default)s)',
                            metavar='INT',
                            default=0,
                            type=int,
@@ -137,7 +137,7 @@ def parseArguments():
 
     filtering.add_argument('--maxFragmentLength',
                            help='The maximum fragment length needed for read/pair '
-                           'inclusion.',
+                           'inclusion. A value of 0 indicates no limit. (Default: %(default)s)',
                            metavar='INT',
                            default=0,
                            type=int,

deeptools/bamCompare.py

@@ -85,7 +85,7 @@ def getOptionalArgs():
                           'If a method is specified, then it will be used to compensate '
                           'for sequencing depth differences between the samples. '
                           'As an alternative, this can be set to None and an option from '
-                          '--normalizeUsing <method> can be used.',
+                          '--normalizeUsing <method> can be used. (Default: %(default)s)',
                           choices=['readCount', 'SES', 'None'],
                           default='readCount')
 
@@ -97,14 +97,14 @@ def getOptionalArgs():
                           'If you do not have a good sequencing depth for '
                           'your samples consider increasing the sampling '
                           'regions\' size to minimize the probability '
-                          'that zero-coverage regions are used.',
+                          'that zero-coverage regions are used. (Default: %(default)s)',
                           default=1000,
                           type=int)
 
     optional.add_argument('--numberOfSamples', '-n',
                           help='*Only relevant when SES is chosen for the '
                           'scaleFactorsMethod.* Number of samplings taken '
-                          'from the genome to compute the scaling factors.',
+                          'from the genome to compute the scaling factors. (Default: %(default)s)',
                           default=1e5,
                           type=int)
 
@@ -125,7 +125,7 @@ def getOptionalArgs():
                           'values are interpreted as negative fold changes. '
                           'Instead of performing a computation using both files, the scaled signal can '
                           'alternatively be output for the first or second file using '
-                          'the \'--operation first\' or \'--operation second\'',
+                          'the \'--operation first\' or \'--operation second\'. (Default: %(default)s)',
                           default='log2',
                           choices=['log2', 'ratio', 'subtract', 'add', 'mean',
                                    'reciprocal_ratio', 'first', 'second'],
@@ -137,7 +137,7 @@ def getOptionalArgs():
                           'You can specify different values as pseudocounts for '
                           'the numerator and the denominator by providing two '
                           'values (the first value is used as the numerator '
-                          'pseudocount and the second the denominator pseudocount).',
+                          'pseudocount and the second the denominator pseudocount). (Default: %(default)s)',
                           default=[1],
                           type=float,
                           nargs='+',

deeptools/bamCoverage.py

@@ -67,7 +67,7 @@ def get_optional_args():
 
     optional.add_argument('--scaleFactor',
                           help='The computed scaling factor (or 1, if not applicable) will '
-                          'be multiplied by this.',
+                          'be multiplied by this. (Default: %(default)s)',
                           default=1.0,
                           type=float,
                           required=False)

deeptools/bamPEFragmentSize.py

@@ -51,7 +51,7 @@ def parse_arguments():
 
     parser.add_argument('--numberOfProcessors', '-p',
                         help='Number of processors to use. The default is '
-                        'to use 1.',
+                        'to use 1. (Default: %(default)s)',
                         metavar="INT",
                         type=int,
                         default=1,
@@ -65,10 +65,10 @@ def parse_arguments():
                         nargs='+')
     parser.add_argument('--plotTitle', '-T',
                         help='Title of the plot, to be printed on top of '
-                        'the generated image. Leave blank for no title.',
+                        'the generated image. Leave blank for no title. (Default: %(default)s)',
                         default='')
     parser.add_argument('--maxFragmentLength',
-                        help='The maximum fragment length in the histogram. A value of 0 (the default) indicates to use twice the mean fragment length',
+                        help='The maximum fragment length in the histogram. A value of 0 (the default) indicates to use twice the mean fragment length. (Default: %(default)s)',
                         default=0,
                         type=int)
     parser.add_argument('--logScale',
@@ -76,7 +76,7 @@ def parse_arguments():
                         action='store_true')
     parser.add_argument('--binSize', '-bs',
                         metavar='INT',
-                        help='Length in bases of the window used to sample the genome. (default 1000)',
+                        help='Length in bases of the window used to sample the genome. (Default: %(default)s)',
                         default=1000,
                         type=int)
     parser.add_argument('--distanceBetweenBins', '-n',
@@ -87,7 +87,7 @@ def parse_arguments():
                         'for high coverage samples, while smaller values are useful for '
                         'lower coverage samples. Note that if you specify a value that '
                         'results in too few (<1000) reads sampled, the value will be '
-                        'decreased. (default 1000000)',
+                        'decreased. (Default: %(default)s)',
                         default=1000000,
                         type=int)
     parser.add_argument('--blackListFileName', '-bl',

deeptools/bigwigCompare.py

@@ -54,7 +54,7 @@ def parse_arguments(args=None):
                         'You can specify different values as pseudocounts for '
                         'the numerator and the denominator by providing two '
                         'values (the first value is used as the numerator '
-                        'pseudocount and the second the denominator pseudocount).',
+                        'pseudocount and the second the denominator pseudocount). (Default: %(default)s)',
                         default=1,
                         nargs='+',
                         action=parserCommon.requiredLength(1, 2),
@@ -73,11 +73,10 @@ def parse_arguments(args=None):
                         'the negative of the inverse of the ratio '
                         'if the ratio is less than 0. The resulting '
                         'values are interpreted as negative fold changes. '
-                        '*NOTE*: Only with --operation subtract can --normalizeUsing RPGC or '
-                        '--normalizeUsing RPKM be used. Instead of performing a '
+                        'Instead of performing a '
                         'computation using both files, the scaled signal can '
                         'alternatively be output for the first or second file using '
-                        'the \'--operation first\' or \'--operation second\'',
+                        'the \'--operation first\' or \'--operation second\' (Default: %(default)s)',
                         default='log2',
                         choices=['log2', 'ratio', 'subtract', 'add', 'mean',
                                  'reciprocal_ratio', 'first', 'second'],

deeptools/computeGCBias.py

@@ -94,7 +94,7 @@ def getRequiredArgs():
 
     optional.add_argument('--sampleSize',
                           default=5e7,
-                          help='Number of sampling points to be considered.',
+                          help='Number of sampling points to be considered. (Default: %(default)s)',
                           type=int)
 
     optional.add_argument('--extraSampling',
@@ -130,7 +130,7 @@ def getRequiredArgs():
                       'standard fragment size for Illumina machines. However, '
                       'if the depth of sequencing is low, a larger bin size '
                       'will be required, otherwise many bins will not '
-                      'overlap with any read')
+                      'overlap with any read (Default: %(default)s)')
 
     return parser
 

deeptools/computeMatrix.py

@@ -144,7 +144,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                               default=1000,
                               type=int,
                               help='Distance in bases to which all regions will '
-                              'be fit.')
+                              'be fit. (Default: %(default)s)')
         optional.add_argument('--startLabel',
                               default='TSS',
                               help='Label shown in the plot for the start of '
@@ -153,38 +153,38 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                               'e.g. "peak start". Note that this is only '
                               'useful if you plan to plot the results yourself '
                               'and not, for example, with plotHeatmap, which '
-                              'will override this.')
+                              'will override this. (Default: %(default)s)')
         optional.add_argument('--endLabel',
                               default='TES',
                               help='Label shown in the plot for the region '
                               'end. Default is TES (transcription end site). '
                               'See the --startLabel option for more '
-                              'information. ')
+                              'information. (Default: %(default)s) ')
         optional.add_argument('--beforeRegionStartLength', '-b', '--upstream',
                               default=0,
                               type=int,
                               help='Distance upstream of the start site of '
                               'the regions defined in the region file. If the '
                               'regions are genes, this would be the distance '
-                              'upstream of the transcription start site.')
+                              'upstream of the transcription start site. (Default: %(default)s)')
         optional.add_argument('--afterRegionStartLength', '-a', '--downstream',
                               default=0,
                               type=int,
                               help='Distance downstream of the end site '
                               'of the given regions. If the '
                               'regions are genes, this would be the distance '
-                              'downstream of the transcription end site.')
+                              'downstream of the transcription end site. (Default: %(default)s)')
         optional.add_argument("--unscaled5prime",
                               default=0,
                               type=int,
                               help='Number of bases at the 5-prime end of the '
                               'region to exclude from scaling. By default, '
-                              'each region is scaled to a given length (see the --regionBodyLength option). In some cases it is useful to look at unscaled signals around region boundaries, so this setting specifies the number of unscaled bases on the 5-prime end of each boundary.')
+                              'each region is scaled to a given length (see the --regionBodyLength option). In some cases it is useful to look at unscaled signals around region boundaries, so this setting specifies the number of unscaled bases on the 5-prime end of each boundary. (Default: %(default)s)')
         optional.add_argument("--unscaled3prime",
                               default=0,
                               type=int,
                               help='Like --unscaled5prime, but for the 3-prime '
-                              'end.')
+                              'end. (Default: %(default)s)')
 
     elif case == 'reference-point':
         optional.add_argument('--referencePoint',
@@ -195,7 +195,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                               'region end (TES) or the center of the region. '
                               'Note that regardless of what you specify, '
                               'plotHeatmap/plotProfile will default to using "TSS" as the '
-                              'label.')
+                              'label. (Default: %(default)s)')
 
         # set region body length to zero for reference point mode
         optional.add_argument('--regionBodyLength', help=argparse.SUPPRESS,
@@ -207,13 +207,13 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                               type=int,
                               metavar='INT bp',
                               help='Distance upstream of the reference-point '
-                              'selected.')
+                              'selected. (Default: %(default)s)')
         optional.add_argument('--afterRegionStartLength', '-a', '--downstream',
                               default=1500,
                               metavar='INT bp',
                               type=int,
                               help='Distance downstream of the '
-                              'reference-point selected.')
+                              'reference-point selected. (Default: %(default)s)')
         optional.add_argument('--nanAfterEnd',
                               action='store_true',
                               help='If set, any values after the region end '
@@ -225,7 +225,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
     optional.add_argument('--binSize', '-bs',
                           help='Length, in bases, of the non-overlapping '
                           'bins for averaging the score over the '
-                          'regions length.',
+                          'regions length. (Default: %(default)s)',
                           type=int,
                           default=10)
 
@@ -240,7 +240,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                           'the input files. If you require the output order to '
                           'match that of the input regions, then either specify '
                           '"keep" or use computeMatrixOperations to resort the '
-                          'results file.',
+                          'results file. (Default: %(default)s)',
                           choices=["descend", "ascend", "no", "keep"],
                           default='keep')
 
@@ -249,7 +249,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                           'sorting. The value is computed for each row.'
                           'Note that the region_length option will lead '
                           'to a dotted line within the heatmap that indicates '
-                          'the end of the regions.',
+                          'the end of the regions. (Default: %(default)s)',
                           choices=["mean", "median", "max", "min", "sum",
                                    "region_length"],
                           default='mean')
@@ -268,7 +268,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                           help='Define the type of statistic that should be '
                           'used over the bin size range. The '
                           'options are: "mean", "median", "min", "max", "sum" '
-                          'and "std". The default is "mean".')
+                          'and "std". The default is "mean". (Default: %(default)s)')
 
     optional.add_argument('--missingDataAsZero',
                           help='If set, missing data (NAs) will be treated as zeros. '
@@ -291,7 +291,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                           'will be skipped. This is useful to skip, '
                           'for example, genes where the read count is zero '
                           'for any of the bins. This could be the result of '
-                          'unmappable areas and can bias the overall results.')
+                          'unmappable areas and can bias the overall results. (Default: %(default)s)')
 
     optional.add_argument('--maxThreshold',
                           default=None,
@@ -301,7 +301,7 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
                           'will be skipped. The maxThreshold is useful to '
                           'skip those few regions with very high read counts '
                           '(e.g. micro satellites) that may bias the average '
-                          'values.')
+                          'values. (Default: %(default)s)')
 
     optional.add_argument('--blackListFileName', '-bl',
                           help="A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered.",
@@ -336,13 +336,13 @@ def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
 
     optional.add_argument('--scale',
                           help='If set, all values are multiplied by '
-                          'this number.',
+                          'this number. (Default: %(default)s)',
                           type=float,
                           default=1)
     optional.add_argument('--numberOfProcessors', '-p',
                           help='Number of processors to use. Type "max/2" to '
                           'use half the maximum number of processors or "max" '
-                          'to use all available processors.',
+                          'to use all available processors. (Default: %(default)s)',
                           metavar="INT",
                           type=numberOfProcessors,
                           default=1,

deeptools/computeMatrixOperations.py

@@ -270,7 +270,7 @@ def sortArgs():
                           default='transcript',
                           help='When a GTF file is used to provide regions, only '
                           'entries with this value as their feature (column 2) '
-                          'will be processed as transcripts.')
+                          'will be processed as transcripts. (Default: %(default)s)')
 
     optional.add_argument('--transcript_id_designator',
                           default='transcript_id',
@@ -281,7 +281,7 @@ def sortArgs():
                           '\'transcript_id "ACTB"\', for a key of transcript_id '
                           'and a value of ACTB). In some cases it can be '
                           'convenient to use a different identifier. To do so, set '
-                          'this to the desired key.')
+                          'this to the desired key. (Default: %(default)s)')
 
     return parser
 
@@ -679,6 +679,8 @@ def sortMatrix(hm, regionsFileName, transcriptID, transcript_id_designator, verb
             if not labelColumn:
                 labelColumn = dti.getLabel(line)
             line = dti.getNext(fp)
+        while line.startswith("track "):
+            line = dti.getNext(fp)
 
         # Find the label column
         subtract = 0

deeptools/correlation.py

@@ -299,8 +299,8 @@ class Correlation:
         # a good contrast between the correlation numbers that are
         # plotted on black.
         if plot_numbers:
-            cmap = cmap.from_list(colormap + "clipped",
-                                  cmap(np.linspace(0, 0.9, 10)))
+            cmap = pltcolors.LinearSegmentedColormap.from_list(colormap + "clipped",
+                                                               cmap(np.linspace(0, 0.9, 10)))
 
         cmap.set_under((0., 0., 1.))
         # Plot distance matrix.

deeptools/correlation_heatmap.py

@@ -4,6 +4,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import scipy.cluster.hierarchy as sch
 from matplotlib import rcParams
+import matplotlib.colors as pltcolors
 
 rcParams['pdf.fonttype'] = 42
 rcParams['svg.fonttype'] = 'none'
@@ -50,8 +51,8 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,
     # a good contrast between the correlation numbers that are
     # plotted on black.
     if plot_numbers:
-        cmap = cmap.from_list(colormap + "clipped",
-                              cmap(np.linspace(0, 0.9, 10)))
+        cmap = pltcolors.LinearSegmentedColormap.from_list(colormap + "clipped",
+                                                           cmap(np.linspace(0, 0.9, 10)))
 
     cmap.set_under((0., 0., 1.))
     # Plot distance matrix.