INNER CODE UNIT · Python
parse_arguments
deeptools/HiCExplorer · hicexplorer/chicAggregateStatistic.py:23
def parse_arguments(args=None):
parser = argparse.ArgumentParser(add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter,
description="""
chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one
file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one
target file for all viewpoints is accepted.
"""
)
parserRequired = parser.add_argument_group('Required arguments')
parserRequired.add_argument('--interactionFile', '-if',
help='path to the interaction files which should be used for aggregation of the statistics.',
required=True)
parserRequired.add_argument('--targetFile', '-tf',
help='path to the target files which contains the target regions to prepare data for differential analysis. This is either the target file in the hdf format created by chicSignificantInteractions or a regular, three column bed file.'
)