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/PeakCalling/yeast/call_peaks.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(
        "yeast_call_peaks",
        help=script_desc,
        prog="yeast_call_peaks",
        parents=[common_args],
    )

    parser.set_defaults(func=main)

    parser.add_argument(
        "--experiment_data_paths",
        type=str,
        nargs="+",
        help="paths to the experiment data files.",
        required=True,
    )
    parser.add_argument(
        "--experiment_orig_chr_convention",
        type=str,
        help="the chromosome naming convention used in the experiment data " "file.",
        required=True,
    )
    parser.add_argument(
        "--promoter_data_path",
        type=str,
        help="path to the promoter data file.",
        required=True,
    )
    parser.add_argument(
        "--promoter_orig_chr_convention",
        type=str,
        help="the chromosome naming convention used in the promoter data " "file.",
        required=True,
    )
    parser.add_argument(
        "--background_data_path",
        type=str,
        help="path to the background data file.",
        required=True,
    )
    parser.add_argument(
        "--background_orig_chr_convention",
        type=str,
        help="the chromosome naming convention used in the background data " "file.",
        required=True,
    )
    parser.add_argument(
        "--chrmap_data_path",
        type=str,
        help="path to the chromosome map file. this must include the data "
        "files' current naming conventions, the desired naming, and a column "
        "`type` that indicates whether the chromosome is 'genomic' or "
        "something else, eg 'mitochondrial' or 'plasmid'.",
        required=True,
    )
    parser.add_argument(
        "--unified_chr_convention",
        type=str,
        help="the chromosome naming convention to use in the output " "DataFrame.",
        required=False,
        default="ucsc",
    )
    parser.add_argument(
        "--deduplicate_experiment",
        action="store_true",
        help="set this flag to deduplicate the experiment data based on `chr`, "
        "`start` and `end` such that if an insertion is found at the same "
        "coordinate on different strands, only one of those records will be "
        "retained.",
    )
    parser.add_argument(
        "--genomic_only",
        action="store_true",
        help="set this flag to include only genomic chromosomes in the "
        "experiment and background.",
    )
    parser.add_argument(
        "--output_path",
        default="sig_results.csv",
        type=str,
        help="path to the output file.",
    )
    parser.add_argument(
        "--pseudocount",
        type=float,
        help="pseudocount to use when calculating poisson pvalue. Note that "
        "this is used only when the background hops are 0 for a given promoter.",
        required=False,
        default=0.1,
    )
    parser.add_argument(
        "--compress_output",
        action="store_true",
        help="set this flag to gzip the output csv file.",
    )

    return subparser