INNER CODE UNIT · Python

process_kegg

BortonWrightonLabs/DRAM · bin/format_kegg_database.py:55

def process_kegg(
    kegg_loc,
    output_dir,
    gene_ko_link_loc=None,
    download_date=None,
    threads=10,
):
    threads = threads or 10  # make sure cli option is >=1 and not None
    if not download_date:
        download_date = get_iso_date()
    if gene_ko_link_loc is not None and Path(gene_ko_link_loc).exists():
        # add KOs to end of header where KO is not already there
        kegg_mod_loc = path.join(output_dir, "kegg.mod.fa")
        write_sequence(
            generate_modified_kegg_fasta(kegg_loc, gene_ko_link_loc),
            format="fasta",
            into=kegg_mod_loc,
        )

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