def test_interleave(self):
'It interleaves two iterators with paired reads'
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = list(read_seqs([open(file1)], 'fastq'))
rev_seqs = list(read_seqs([open(file2)], 'fastq'))
try:
list(interleave_pairs(fwd_seqs, rev_seqs))
self.fail('InterleaveError expected')
except InterleaveError:
pass
# we skip the tests
seqs = list(interleave_pairs(fwd_seqs, rev_seqs, skip_checks=True))
assert len(seqs) == 8
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend1b.sfastq')
fwd_seqs = read_seqs([open(file1)], 'fastq')
rev_seqs = read_seqs([open(file2)], 'fastq')
seqs = list(interleave_pairs(fwd_seqs, rev_seqs))
assert len(seqs) == 8
def test_interleave(self):
'It interleaves two iterators with paired reads'
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = list(read_seqs([open(file1)], 'fastq'))
rev_seqs = list(read_seqs([open(file2)], 'fastq'))
try:
list(interleave_pairs(fwd_seqs, rev_seqs))
self.fail('InterleaveError expected')
except InterleaveError:
pass
# we skip the tests
seqs = list(interleave_pairs(fwd_seqs, rev_seqs, skip_checks=True))
assert len(seqs) == 8
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend1b.sfastq')
fwd_seqs = read_seqs([open(file1)], 'fastq')
rev_seqs = read_seqs([open(file2)], 'fastq')
seqs = list(interleave_pairs(fwd_seqs, rev_seqs))
assert len(seqs) == 8
def test_deinterleave(self):
'It de-interleaves an iterator of alternating fwd and rev reads'
fhand1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
fhand2 = os.path.join(TEST_DATA_DIR, 'pairend1b.sfastq')
fwd_seqs = read_seqs([open(fhand1)], 'fastq')
rev_seqs = read_seqs([open(fhand2)], 'fastq')
seqs = interleave_pairs(fwd_seqs, rev_seqs)
out_fhand1 = StringIO()
out_fhand2 = StringIO()
out_format = 'fastq'
deinterleave_pairs(seqs, out_fhand1, out_fhand2, out_format)
result1 = out_fhand1.getvalue()
result2 = out_fhand2.getvalue()
assert result1.strip() == open(fhand1).read().strip()
assert result2.strip() == open(fhand2).read().strip()
def test_deinterleave(self):
'It de-interleaves an iterator of alternating fwd and rev reads'
fhand1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
fhand2 = os.path.join(TEST_DATA_DIR, 'pairend1b.sfastq')
fwd_seqs = read_seqs([open(fhand1)], 'fastq')
rev_seqs = read_seqs([open(fhand2)], 'fastq')
seqs = interleave_pairs(fwd_seqs, rev_seqs)
out_fhand1 = StringIO()
out_fhand2 = StringIO()
out_format = 'fastq'
deinterleave_pairs(seqs, out_fhand1, out_fhand2, out_format)
result1 = out_fhand1.getvalue()
result2 = out_fhand2.getvalue()
assert result1.strip() == open(fhand1).read().strip()
assert result2.strip() == open(fhand2).read().strip()
