def gather_paired(stream, **kw): itr = BrokenPairedReader(stream, **kw) x = [] m = 0 num = 0 for num, is_pair, read1, read2 in itr: x.append((read1.name if read1 is not None else None, read2.name if read2 is not None else None)) m += 1 return x, num, m
def testRequirePairedAndMinLength_NeitherPass(self, parser, create_fastx): reads = [ Sequence('seq1/1', 'A' * 5), Sequence('seq1/2', 'A' * 4), Sequence('seq3/1', 'A' * 3), Sequence('seq3/2', 'A' * 3) ] reader = BrokenPairedReader(parser(create_fastx(reads)), min_length=4, require_paired=True) result = [] for n, paired, first, second in reader: result.append((first, second)) assert n == 0 assert len(result) == 1 l, r = result[0] assert l == reads[0] assert r == reads[1]