INNER CODE UNIT · Python

main

BortonWrightonLabs/DRAM · bin/format_kegg_database.py:145

def main():
    parser = argparse.ArgumentParser(description="Prepare KEGG database")
    parser.add_argument("--kegg_loc", type=str, help="Path to the KEGG fasta file")
    parser.add_argument(
        "--gene_ko_link_loc", type=str, help="Path to the gene KO link file"
    )
    parser.add_argument(
        "--skip_gene_ko_link",
        action="store_true",
        help="Skip gene KO link processing. If not passed in, `--gene_ko_link_loc` is required",
    )
    parser.add_argument(
        "--output_dir", type=str, help="Path to the output directory", default="kegg"
    )
    parser.add_argument(
        "--download_date",
        type=str,
        help="Date of the KEGG download, if not included, will use today's date",

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