INNER CODE UNIT · Python

wrap

steineggerlab/Metabuli · util/simulate_faa_reads.py:32

def wrap(seq, width=80):
    for i in range(0, len(seq), width):
        yield seq[i:i + width]


def main():
    parser = argparse.ArgumentParser(
        description="Naively simulate amino-acid reads by sampling substrings from .faa files."
    )
    parser.add_argument("faa_list", help="Text file with one .faa/.faa.gz path per line.")
    parser.add_argument("output", help="Output FASTA file for simulated reads.")
    parser.add_argument("--reads", type=int, default=10000, help="Number of reads to emit.")
    parser.add_argument("--read-len", type=int, default=100, help="Substring length.")
    parser.add_argument("--files", type=int, default=100, help="Number of input files to sample.")
    parser.add_argument("--seed", type=int, default=1, help="Random seed for reproducible output.")
    args = parser.parse_args()

    rng = random.Random(args.seed)

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