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Merge pull request #629 from deeptools/develop
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‎azure-pipelines.yml‎

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python.version: '3.6'
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Python37:
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python.version: '3.7'
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Python38:
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python.version: '3.8'
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steps:
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- bash: |
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python.version: '3.6'
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Python37:
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python.version: '3.7'
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Python38:
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python.version: '3.8'
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- bash: |

‎docs/conf.py‎

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'mpl_toolkits', 'mpl_toolkits.axisartist', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1',
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'Bio', 'Bio.Seq', 'Bio.Alphabet', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
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'future.utils', 'cooler', 'logging', 'unidecode', 'hic2cool', 'hicmatrix', 'hicmatrix.HiCMatrix',
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'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt']
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'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster']
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for mod_name in MOCK_MODULES:
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sys.modules[mod_name] = Mock()

‎docs/content/News.rst‎

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11
News and Developments
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=====================
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Release 3.6
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-----------
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**10 November 2020**
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- hicAggregateContacts, thanks @LeilyR:
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- hicAggragateContact has been updated to be able to handle inter chromosomal contacts as well as inter chromosomal contacts
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- Added scikit-learn to dependencies
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- hicBuildMatrix: Fixing another bug concerning scaffolds without any restriction enzyme cut site
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- Updated dependencies
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- Adding default values to the documentation. Thanks @lldelisle
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- hicTransform: Fixing a bug in case one of the intermediate matrices is empty
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- Official Python 3.8 support:
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- Manually setting 'fork' as the start method for multiprocessing because the default on macOS was set to 'spawn'
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Release 3.5.3
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-------------
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**14 October 2020**
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- Bug fix release:
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- Reads from scaffolds without any restriction enzym cut site are considered as 'same fragment'. An appearance of such a read will not lead to a crash anymore
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- Reads from scaffolds without any restriction enzyme cut site are considered as 'same fragment'. An appearance of such a read will not lead to a crash anymore
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- Minor documentation improvements
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‎docs/content/citation.rst‎

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Citation
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========
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Please cite HiCExplorer as follows:
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Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning.
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**Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research**, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220
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Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning.
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**Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization**, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504
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Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening,Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke.
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**"High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications**, Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w

‎docs/content/tools/hicAggregateContacts.rst‎

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@@ -28,7 +28,7 @@ Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosop
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$ hicAggregateContacts --matrix Dmel.h5 --BED ChIP-seq-peaks.bed \
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--outFileName Dmel_aggregate_Contacts --vMin 0.8 --vMax 2.2 \
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--range 300000:1000000 --numberOfBins 30 --chromosomes X \
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--avgType mean --transform obs/exp
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--operationType mean --transform obs/exp --mode intra-chr
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.. image:: ../../images/hicAggregateContacts.png
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‎docs/index.rst‎

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content/list-of-tools
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content/example_usage
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content/News
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content/citation
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Citation

‎hicexplorer/__init__.py‎

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warnings.simplefilter(action="ignore", category=RuntimeWarning)
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warnings.simplefilter(action="ignore", category=PendingDeprecationWarning)
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import multiprocessing as mp
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mp.set_start_method('fork')

‎hicexplorer/chicAggregateStatistic.py‎

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parserOpt = parser.add_argument_group('Optional arguments')
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parserOpt.add_argument('--outFileNameSuffix', '-suffix',
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help='File name suffix to save the result.',
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help='File name suffix to save the result'
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' (Default: %(default)s).',
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required=False,
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default='_aggregate_target.txt')
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parserOpt.add_argument('--interactionFileFolder', '-iff',
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help='Folder where the interaction files are stored. Applies only for batch mode.',
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help='Folder where the interaction files are stored. Applies only for batch mode'
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' (Default: %(default)s).',
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required=False,
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default='.')
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parserOpt.add_argument('--targetFileFolder', '-tff',
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help='Folder where the target files are stored. Applies only for batch mode.',
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required=False)
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parserOpt.add_argument('--outputFolder', '-o',
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help='Output folder containing the files.',
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help='Output folder containing the files'
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' (Default: %(default)s).',
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required=False,
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default='aggregatedFiles')
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parserOpt.add_argument('--writeFileNamesToFile', '-w',
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help='',
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help='(Default: %(default)s).',
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default='aggregatedFilesBatch.txt')
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parserOpt.add_argument('--batchMode', '-bm',
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help='turns on batch mode. The files provided by --interactionFile and/or --targetFile contain a list of the files to be processed.',
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required=False,
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action='store_true')
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parserOpt.add_argument('--threads', '-t',
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help='Number of threads (uses the python multiprocessing module). ',
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help='Number of threads (uses the python multiprocessing module)ist'
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' (Default: %(default)s).',
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required=False,
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default=4,
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type=int

‎hicexplorer/chicDifferentialTest.py‎

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parserRequired.add_argument('--alpha', '-a',
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help='define a significance level (alpha) for accepting samples',
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type=float,
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default=0.05,
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required=True)
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parserOpt = parser.add_argument_group('Optional arguments')
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parserOpt.add_argument('--interactionFileFolder', '-iff',
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help='Folder where the interaction files are stored. Applies only for batch mode.',
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help='Folder where the interaction files are stored. Applies only for batch mode'
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' (Default: %(default)s).',
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required=False,
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default='.')
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parserOpt.add_argument('--outputFolder', '-o',
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help='Output folder of the files.',
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help='Output folder of the files'
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' (Default: %(default)s).',
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required=False,
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default='differentialResults')
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parserOpt.add_argument('--statisticTest',
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help='Type of test used: fisher\'s exact test or chi2 contingency',
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help='Type of test used: fisher\'s exact test or chi2 contingency'
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' (Default: %(default)s).',
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choices=['fisher', 'chi2'],
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default='fisher')
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parserOpt.add_argument('--batchMode', '-bm',
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help='turn on batch mode. The given file for --interactionFile and or --targetFile contain a list of the to be processed files.',
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required=False,
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action='store_true')
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parserOpt.add_argument('--threads', '-t',
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help='Number of threads (uses the python multiprocessing module)',
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help='Number of threads (uses the python multiprocessing module)'
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' (Default: %(default)s).',
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required=False,
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default=4,
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type=int
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)
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parserOpt.add_argument('--rejectedFileNamesToFile', '-r',
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help='Writes the names of the rejected H0 (therefore containing the differential interactions) to file. Can be used for batch processing mode of chicPlotViewpoint.',
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help='Writes the names of the rejected H0 (therefore containing the differential interactions) to file. Can be used for batch processing mode of chicPlotViewpoint.'
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' (Default: %(default)s).',
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default='rejected_H0.txt')
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parserOpt.add_argument("--help", "-h", action="help",
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help="show this help message and exit")

‎hicexplorer/chicPlotViewpoint.py‎

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'Format is --region upstream downstream, e.g.: --region 500000 500000 plots 500kb up- and 500kb downstream. This value should not exceed the range used in the other chic-tools.',
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required=True,
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type=int,
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default=[500000, 500000],
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nargs=2)
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parserOpt = parser.add_argument_group('Optional arguments')
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help='path to the background file which should be used for plotting',
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required=False)
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parserOpt.add_argument('--interactionFileFolder', '-iff',
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help='Folder where the interaction files are stored. Applies only for batch mode.',
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help='Folder where the interaction files are stored. Applies only for batch mode'
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' (Default: %(default)s).',
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required=False,
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default='.')
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parserOpt.add_argument('--differentialTestResult', '-dif',
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help='Path to the H0 rejected files to highlight the regions in the plot.',
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required=False,
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nargs='+')
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parserOpt.add_argument('--significantInteractionFileFolder', '-siff',
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help='Folder where the files with detected significant interactions are stored. Applies only for batch mode.',
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help='Folder where the files with detected significant interactions are stored. Applies only for batch mode'
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' (Default: %(default)s).',
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required=False,
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default='.')
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parserOpt.add_argument('--differentialTestResultsFolder', '-diff',
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help='Folder where the H0 rejected files are stored. Applies only for batch mode.',
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help='Folder where the H0 rejected files are stored. Applies only for batch mode'
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' (Default: %(default)s).',
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required=False,
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parserOpt.add_argument('--significantInteractions', '-si',
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parserOpt.add_argument('--outputFolder', '-of',
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help='Output folder of the files.',
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help='Output folder of the files'
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' (Default: %(default)s).',
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required=False,
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default='.')
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parserOpt.add_argument('--outputFormat', '-format',
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help='Output format of the plot.',
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help='Output format of the plot'
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' (Default: %(default)s).',
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required=False,
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default='png')
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parserOpt.add_argument('--dpi',
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help='Optional parameter: Resolution for the image, if'
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'output is a raster graphics image (e.g png, jpg)',
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'output is a raster graphics image (e.g png, jpg)'
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' (Default: %(default)s).',
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type=int,
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required=False)
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parserOpt.add_argument('--binResolution', '-r',
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help='Resolution of the bin in genomic units. Values are set as number of bases, e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.',
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help='Resolution of the bin in genomic units. Values are set as number of bases, e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution'
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' (Default: %(default)s).',
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type=int,
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default=1000,
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required=False)
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parserOpt.add_argument('--colorMapPvalue',
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help='Color map to use for the p-value. Available '
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'values can be seen here: '
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'http://matplotlib.org/examples/color/colormaps_reference.html',
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'http://matplotlib.org/examples/color/colormaps_reference.html'
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' (Default: %(default)s).',
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default='RdYlBu')
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parserOpt.add_argument('--maxPValue', '-map',
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help='Maximal value for p-value. Values above this threshold are set to this value.',
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help='Maximal value for p-value. Values above this threshold are set to this value'
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' (Default: %(default)s).',
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type=float,
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default=0.1)
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parserOpt.add_argument('--minPValue', '-mp',
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help='Minimal value for p-value. Values below this threshold are set to this value.',
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help='Minimal value for p-value. Values below this threshold are set to this value'
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' (Default: %(default)s).',
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type=float,
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default=0.0)
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required=False,
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action='store_true')
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parserOpt.add_argument('--plotSampleNumber', '-psn',
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help='Number of samples per plot. Applies only in batch mode.',
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help='Number of samples per plot. Applies only in batch mode'
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' (Default: %(default)s).',
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required=False,
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default=2,
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type=int)
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parserOpt.add_argument('--colorList', '-cl',
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help='Colorlist for the viewpoint lines.',
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help='Colorlist for the viewpoint lines (Default g b c m y k).',
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required=False,
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default=['g', 'b', 'c', 'm', 'y', 'k'],
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type=str,
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nargs='+')
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parserOpt.add_argument('--threads', '-t',
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help='Number of threads (uses the python multiprocessing module).',
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help='Number of threads (uses the python multiprocessing module)'
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' (Default: %(default)s).',
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required=False,
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default=4,
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type=int

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