parse_args

Parse the command line arguments.

:param subparser: the subparser object. :type subparser: argparse.ArgumentParser :param script_desc: the description of the script. :type script_desc: str :param common_args: the common arguments. :type common_args: argparse.ArgumentParser :return: the parser. :rtype: argparse.ArgumentParser

Source code in callingcardstools/Analysis/yeast/chipexo_promoter_sig.py

def parse_args(
        subparser: argparse.ArgumentParser,
        script_desc: str,
        common_args: argparse.ArgumentParser) -> argparse.ArgumentParser:
    """
    Parse the command line arguments.

    :param subparser: the subparser object.
    :type subparser: argparse.ArgumentParser
    :param script_desc: the description of the script.
    :type script_desc: str
    :param common_args: the common arguments.
    :type common_args: argparse.ArgumentParser
    :return: the parser.
    :rtype: argparse.ArgumentParser
    """

    parser = subparser.add_parser(
        'chipexo_promoter_sig',
        help=script_desc,
        prog='chipexo_promoter_sig',
        parents=[common_args]
    )

    parser.set_defaults(func=main)

    parser.add_argument(
        '--chipexo_data_path',
        help='Path to the chipexo data file.',
        required=True
    )
    parser.add_argument(
        '--chipexo_orig_chr_convention',
        help='Chromosome convention of the chipexo data file.',
        required=True
    )
    parser.add_argument(
        '--promoter_data_path',
        help='Path to the promoter data file.',
        required=True
    )
    parser.add_argument(
        '--promoter_orig_chr_convention',
        help='Chromosome convention of the promoter data file.',
        required=True
    )
    parser.add_argument(
        '--chrmap_data_path',
        help='Path to the chromosome map file.',
        required=True
    )
    parser.add_argument(
        '--unified_chr_convention',
        help='Chromosome convention to convert to.',
        required=True
    )
    parser.add_argument(
        '--output_file',
        default="chipexo_promoter_sig.csv",
        help='Path to the output file.'
    )
    parser.add_argument(
        '--compress',
        action='store_true',
        help='Set this flag to gzip the output file.'
    )

    return subparser