INNER CODE UNIT · Python

seq

BirolLab/straglr · extract_repeats.py:47

                    seq = left_seq + repeat_seq + right_seq
                    seqs[locus].append((aln.query_name, support[locus][aln.query_name][1], seq))
                except:
                    print('problem extracting repeat from {}'.format(aln.query_name))

    return seqs

def report(seqs, out_fa):
    with open(out_fa, 'w') as out:
        for locus in sorted(seqs.keys()):
            for read_name, repeat_size, seq in seqs[locus]:
                out.write('>{} {} {}\n{}\n'.format(read_name, locus, repeat_size, seq))

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")

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