def test_only_barcode5_1_mismatch(self):
# Only barcode5, one mismatch
demultiplex.run(self.fq_fname,
self.adapter,
self.barcodes5[:2],
mismatches=1,
out_dir=self.dir)
demux_file = 'demux_{}.fastq.gz'.format(self.barcodes5[0])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list[0], ['@header1:rbc:GGG/1'])
self.assertEqual(fq_list[1], [self.entry1.seq[6:-10]])
self.assertEqual(fq_list[3], [self.entry1.qual[6:-10]])
demux_file = 'demux_{}.fastq.gz'.format(self.barcodes5[1])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list[0], ['@header2:rbc:AA'])
self.assertEqual(fq_list[1], [self.entry2.seq[5:-10]])
self.assertEqual(fq_list[3], [self.entry2.qual[5:-10]])
self.assertEqual(fq_list[4], ['@header3:rbc:TT'])
self.assertEqual(fq_list[5], [self.entry3.seq[5:-10]])
self.assertEqual(fq_list[7], [self.entry3.qual[5:-10]])
demux_file = 'demux_{}.fastq.gz'.format('nomatch5')
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list, [])
def test_run_fail(self):
message = r'Output directory does not exist. Make sure it does.'
with self.assertRaisesRegex(FileNotFoundError, message):
demultiplex.run(self.reads,
self.adapter,
self.barcodes,
mismatches=1,
out_dir='/unexisting/dir')
def test_both_barcodes_1_mismatch(self):
# Both: barcode5 & barcode3, one mismatch
demultiplex.run(self.fq_fname,
self.adapter,
self.barcodes5,
barcodes3=self.barcodes3,
mismatches=1,
out_dir=self.dir)
demux_file = 'demux_{}.fastq.gz'.format(self.barcodes5[0])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list[0], ['@header1:rbc:GGG/1'])
self.assertEqual(fq_list[1], [self.entry1.seq[6:-10]])
self.assertEqual(fq_list[3], [self.entry1.qual[6:-10]])
demux_file = 'demux_{}_{}.fastq.gz'.format(self.barcodes5[1],
self.barcodes3[1])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(len(fq_list), 4)
self.assertEqual(fq_list[0], ['@header2:rbc:AAAA'])
self.assertEqual(fq_list[1], [self.entry2.seq[5:-15]])
self.assertEqual(fq_list[3], [self.entry2.qual[5:-15]])
demux_file = 'demux_{}_{}.fastq.gz'.format(self.barcodes5[2],
self.barcodes3[2])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(len(fq_list), 4)
self.assertEqual(fq_list[0], ['@header3:rbc:TTT'])
self.assertEqual(fq_list[1], [self.entry3.seq[5:-14]])
self.assertEqual(fq_list[3], [self.entry3.qual[5:-14]])
demux_file = 'demux_{}.fastq.gz'.format('nomatch5')
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list, [])
demux_file = 'demux_{}_{}.fastq.gz'.format(self.barcodes5[1],
'nomatch')
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list, [])
demux_file = 'no_adapter_found_{}.fastq.gz'.format(self.barcodes5[1])
fq_list = make_list_from_file(os.path.join(self.dir, demux_file))
self.assertEqual(fq_list, [])
def test_run_ok(self):
expected = [
'{}/demux_{}.fastq.gz'.format(self.dir, b) for b in self.barcodes
]
expected.extend([self.dir + '/demux_nomatch.fastq.gz'])
# Without adapter
filenames = demultiplex.run(self.reads,
None,
self.barcodes,
mismatches=1,
out_dir=self.dir)
self.assertEqual(sorted(filenames), sorted(expected))
# With adapter
filenames = demultiplex.run(self.reads,
self.adapter,
self.barcodes,
mismatches=1,
out_dir=self.dir)
self.assertEqual(sorted(filenames), sorted(expected))
def test_run_ok_no_adapter(self):
barcodes = ['NNAAAN', 'NNACTN']
data = [
[
'@header/1', 'GGAAAG' + make_sequence(40, rnd_seed=99), '+',
make_quality_scores(50, min_chr=65, max_chr=73, rnd_seed=76) +
'!J'
],
[
'@header2 blah', 'TTCCTT' + make_sequence(40, rnd_seed=47),
'+',
make_quality_scores(50, min_chr=65, max_chr=73, rnd_seed=71) +
'!J'
],
[
'@header3', 'TTGGGT' + make_sequence(40, rnd_seed=13), '+',
make_quality_scores(50, min_chr=65, max_chr=73, rnd_seed=12) +
'!J'
],
]
fq_fname = get_temp_file_name(extension='fq')
fq_file = iCount.files.fastq.FastqFile(fq_fname, 'wt')
for line in data:
fq_file.write(iCount.files.fastq.FastqEntry(*line))
fq_file.close()
demultiplex.run(fq_fname,
None,
barcodes,
mismatches=1,
out_dir=self.dir)
fq1_list = make_list_from_file('{}/demux_{}.fastq.gz'.format(
self.dir, barcodes[0]))
expected1 = [
['@header:rbc:GGG/1'],
[data[0][1][6:]],
['+'],
[data[0][3][6:]],
]
self.assertEqual(fq1_list, expected1)
fq2_list = make_list_from_file('{}/demux_{}.fastq.gz'.format(
self.dir, barcodes[1]))
expected2 = [
['@header2:rbc:TTT'],
[data[1][1][6:]],
['+'],
[data[1][3][6:]],
]
self.assertEqual(fq2_list, expected2)
fq3_list = make_list_from_file('{}/demux_{}.fastq.gz'.format(
self.dir, 'nomatch'))
expected3 = [
['@header3'],
[data[2][1]],
['+'],
[data[2][3]],
]
self.assertEqual(fq3_list, expected3)
def test_run_fail(self):
message = r'Output directory does not exist. Make sure it does.'
with self.assertRaisesRegex(FileNotFoundError, message):
demultiplex.run('reads.fq',
'adapter', ['barcodes'],
out_dir='/unexisting/dir')
