def parse_arguments(args=None):
    parser = argparse.ArgumentParser(
        parents=[parserCommon.heatmapperMatrixArgs(),
                 parserCommon.heatmapperOutputArgs(mode='heatmap'),
                 parserCommon.heatmapperOptionalArgs(mode='heatmap')],
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        description='This tool creates a heatmap for a '
        'score associated to genomic regions. '
        'The program requires a preprocessed matrix '
        'generated by the tool computeMatrix.',
        epilog='An example usage is: plotHeatmap -m <matrix file>',
        add_help=False)

    return parser
Exemple #2
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def parse_arguments(args=None):
    parser = argparse.ArgumentParser(
        parents=[parserCommon.heatmapperMatrixArgs(),
                 parserCommon.heatmapperOutputArgs(mode='heatmap'),
                 parserCommon.heatmapperOptionalArgs(mode='heatmap')],
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        description='This tool creates a heatmap for '
        'scores associated with genomic regions. '
        'The program requires a matrix file '
        'generated by the tool ``computeMatrix``.',
        epilog='An example usage is: plotHeatmap -m <matrix file>',
        add_help=False)

    return parser
Exemple #3
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def parse_arguments(args=None):
    parser = argparse.ArgumentParser(
        parents=[parserCommon.heatmapperMatrixArgs(),
                 parserCommon.heatmapperOutputArgs(mode='profile'),
                 parserCommon.heatmapperOptionalArgs(mode='profile')],
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        description='This tool creates a profile plot for '
        'scores over sets of genomic regions. '
        'Typically, these regions are genes, but '
        'any other regions defined in BED '
        ' will work. A matrix generated '
        'by computeMatrix is required.',
        epilog='An example usage is: plotProfile -m <matrix file>',
        add_help=False)

    return parser
Exemple #4
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def parse_arguments(args=None):
    parser = argparse.ArgumentParser(
        parents=[parserCommon.heatmapperMatrixArgs(),
                 parserCommon.heatmapperOutputArgs(mode='profile'),
                 parserCommon.heatmapperOptionalArgs(mode='profile')],
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        description='This tool creates a profile plot for '
        'scores over sets of genomic regions. '
        'Typically, these regions are genes, but '
        'any other regions defined in BED '
        ' will work. A matrix generated '
        'by computeMatrix is required.',
        epilog='An example usage is: plotProfile -m <matrix file>',
        add_help=False)

    return parser