INNER CODE UNIT · Python
end
BirolLab/straglr · extract_repeats.py:36
start, end = support[locus][aln.query_name][0], support[locus][aln.query_name][0] + support[locus][aln.query_name][1]
else:
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