INNER CODE UNIT · Python

parse_args

hillerlab/TOGA · CESAR_wrapper.py:91

def parse_args():
    """Parse args, check and return."""
    # parse args
    app = argparse.ArgumentParser(description="")
    app.add_argument("gene", type=str, help="working gene")  # mandatory
    app.add_argument(
        "chains",
        type=str,
        help="chain ids, write 'region' if you like to type a region directly",
    )
    app.add_argument(
        "bdb_bed_file", type=str, help="BDB BED FILE, text bed12 also works but slower."
    )
    app.add_argument(
        "bdb_chain_file",
        type=str,
        help="BDB CHAIN FILE" "Or chain file, or even chain.gz file, but slower.",
    )

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