INNER CODE UNIT · Python

create_mmseqs

BortonWrightonLabs/DRAM · bin/format_kegg_database.py:87

def create_mmseqs(fasta_loc, output_loc, threads):
    """Takes a fasta file and makes a mmseqs2 database for use in blast searching and hmm searching with mmseqs2."""
    LOGGER.info(f"Creating MMseqs2 database for {fasta_loc}...")
    subprocess.run(
        ["mmseqs", "createdb", fasta_loc, output_loc],
        check=True,
        stdout=subprocess.DEVNULL,
        stderr=subprocess.DEVNULL,
    )
    tmp_dir = path.join(path.dirname(output_loc), "tmp")
    LOGGER.info(f"Created MMseqs2 database for {fasta_loc}... Now creating index")
    subprocess.run(
        ["mmseqs", "createindex", output_loc, tmp_dir, "--threads", str(threads)],
        check=True,
        stdout=subprocess.DEVNULL,
        stderr=subprocess.DEVNULL,
    )
    LOGGER.info(f"MMseqs2 database created at {output_loc}")

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