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()
def filter_chimeras(ref_fpath, out_fhand, chimeras_fhand, in_fhands,
unknown_fhand, unpaired=False, paired_result=True,
settings=get_setting('CHIMERAS_SETTINGS'),
min_seed_len=None, directory=None):
file_format = get_format(in_fhands[0])
if unpaired:
unpaired_fpaths = [fhand.name for fhand in in_fhands]
paired_fpaths = None
else:
f_fhand = NamedTemporaryFile()
r_fhand = NamedTemporaryFile()
seqs = read_seqs(in_fhands)
deinterleave_pairs(seqs, f_fhand, r_fhand, file_format)
paired_fpaths = [f_fhand.name, r_fhand.name]
unpaired_fpaths = None
bamfile = _sorted_mapped_reads(ref_fpath, paired_fpaths, unpaired_fpaths,
directory, file_format, min_seed_len)
total = 0
chimeric = 0
unknown = 0
for pair, kind in classify_mapped_reads(bamfile, settings=settings,
paired_result=paired_result,
file_format=file_format):
if kind is NON_CHIMERIC:
write_seqs(pair, out_fhand)
elif kind is CHIMERA and chimeras_fhand is not None:
write_seqs(pair, chimeras_fhand)
chimeric += 1
elif kind is UNKNOWN and unknown_fhand is not None:
write_seqs(pair, unknown_fhand)
unknown += 1
total += 1
mapped = total - chimeric - unknown
print 'Total pairs analyzed: ', total
print 'Chimeric pairs filtered: ', chimeric, '\t', chimeric / float(total)
print 'Unknown pairs found: ', unknown, '\t', unknown / float(total)
print 'Non-chimeric pairs: ', mapped, '\t', mapped / float(total)