INNER CODE UNIT · Python

parse_args

BirolLab/straglr · extract_repeats.py:60

def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument("tsv", type=str, help="Straglr tsv")
    parser.add_argument("bam", type=str, help="bam file") 
    parser.add_argument("out", type=str, help="output fasta")
    parser.add_argument("--locus", type=str, help="UCSC-format coordinate")
    parser.add_argument("--flank", type=int, default=100, help="flank size. Default:100")
    args = parser.parse_args()
    return args
    
def main():
    args = parse_args()
    support = parse_tsv(args.tsv, args.locus)
    bam = pysam.AlignmentFile(args.bam)
    seqs = extract_repeats(bam, support, flank_size=args.flank)
    report(seqs, args.out)

main()

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