INNER CODE UNIT · Python

generate_gfa_file

Gabaldonlab/redundans · redundans.py:153

def generate_gfa_file(file, threads="4"):
    """Return a gfa file generated using gfastats"""

    # First process the filename to add the new extension

    abs_path_gfa = os.path.abspath(re.sub(".fa", ".gfa", file))

    with open(abs_path_gfa, "wb") as f:

        args1 = ["gfastats", "-f", file, "--threads", str(threads), "-o", "gfa"]
        proc1 = subprocess.Popen(args1, stderr=subprocess.DEVNULL, stdout=f)
        proc1.communicate()

    if os.path.exists(abs_path_gfa):
        return True
    else:
        return False

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