INNER CODE UNIT · Python

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BirolLab/straglr · extract_repeats.py:38

                    start = rlen - (support[locus][aln.query_name][0] + support[locus][aln.query_name][1])
                    end = start + support[locus][aln.query_name][1]

                try:
                    repeat_seq = aln.query_sequence[start:end].lower()
                    left = max(0, start - flank_size), start
                    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:

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