INNER CODE UNIT · Python

right

BirolLab/straglr · extract_repeats.py:44

                    right = end, min(end + flank_size, rlen)
                    left_seq = aln.query_sequence[left[0]:left[1]].upper()
                    right_seq = aln.query_sequence[right[0]:right[1]].upper()
                    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()

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