def test(self):
expected = [
(Sequence('read1/1 some text', 'TTATTTGTCTCCAGC', '##HHHHHHHHHHHHH'),
Sequence('read1/2 other text', 'GCTGGAGACAAATAA', 'HHHHHHHHHHHHHHH')),
(Sequence('read3/1', 'CCAACTTGATATTAATAACA', 'HHHHHHHHHHHHHHHHHHHH'),
Sequence('read3/2', 'TGTTATTAATATCAAGTTGG', '#HHHHHHHHHHHHHHHHHHH'))
]
reads = list(InterleavedSequenceReader("tests/cut/interleaved.fastq"))
for (r1, r2), (e1, e2) in zip(reads, expected):
print(r1, r2, e1, e2)
assert reads == expected
with openseq("tests/cut/interleaved.fastq", interleaved=True) as f:
reads = list(f)
assert reads == expected
def test_incorrectly_paired(self):
s = StringIO('@r1/1\nACG\n+\nHHH\n@wrong_name\nTTT\n+\nHHH')
list(InterleavedSequenceReader(s))
def test_missing_partner(self):
s = StringIO('@r1\nACG\n+\nHHH')
list(InterleavedSequenceReader(s))