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]