def test_barcode_size_diff(self):
# One mismatch, second barcode.
barcodes = ['NAAANN', 'NNCCCNN']
adapter = 'CCCCCC'
data = [
'@header1',
'TACATT' + adapter + make_sequence(40, rnd_seed=0),
'+',
make_quality_scores(50, rnd_seed=0) + '!J',
'@header2',
'AACCCTT' + adapter + make_sequence(39, rnd_seed=0),
'+',
make_quality_scores(50, rnd_seed=0) + '!J',
]
fq_fname = get_temp_file_name(extension='fq')
fq_file = iCount.files.fastq.FastqFile(fq_fname, 'wt')
fq_file.write(iCount.files.fastq.FastqEntry(*data[:4]))
fq_file.write(iCount.files.fastq.FastqEntry(*data[4:]))
fq_file.close()
handle = demultiplex._extract(fq_fname, barcodes, mismatches=1)
read1, exp_id1, randomer1 = next(handle)
self.assertEqual(exp_id1, 0)
self.assertEqual(randomer1, 'TTT')
self.assertEqual(read1.id, data[0])
self.assertEqual(read1.seq, data[1][6:])
self.assertEqual(read1.plus, '+')
self.assertEqual(read1.qual, data[3][6:])
read2, exp_id2, randomer2 = next(handle)
self.assertEqual(exp_id2, 1)
self.assertEqual(randomer2, 'AATT')
self.assertEqual(read2.id, data[4])
self.assertEqual(read2.seq, data[5][7:])
self.assertEqual(read2.plus, '+')
self.assertEqual(read2.qual, data[7][7:])
def test_barcode_size_diff(self):
# One mismatch, second barcode.
barcodes = demultiplex.prepare_barcodes(self.barcodes5, None)
entry1 = FastqEntry(
'@header1',
'TTAATT' + make_sequence(40),
'+',
make_quality_scores(44),
)
entry2 = FastqEntry(
'@header2',
'GGACGAGG' + make_sequence(40),
'+',
make_quality_scores(48),
)
fq_fname = self.create_fq_file([entry1, entry2])
handle = demultiplex._extract(fq_fname,
barcodes,
mismatches=1,
minimum_length=15)
read1, wbrc, randomer1 = next(handle)
self.assertEqual(wbrc, self.barcodes5[0])
self.assertEqual(randomer1, 'TTT')
self.assertEqual(read1.id, entry1.id)
self.assertEqual(read1.seq, entry1.seq[6:])
self.assertEqual(read1.plus, entry1.plus)
self.assertEqual(read1.qual, entry1.qual[6:])
read2, wbrc, randomer2 = next(handle)
self.assertEqual(wbrc, self.barcodes5[2])
self.assertEqual(randomer2, 'GGGG')
self.assertEqual(read2.id, entry2.id)
self.assertEqual(read2.seq, entry2.seq[8:])
self.assertEqual(read2.plus, entry2.plus)
self.assertEqual(read2.qual, entry2.qual[8:])
def test_extract_mismatch(self):
# To many mismatches
barcodes = demultiplex.prepare_barcodes(self.barcodes5, None)
entry = FastqEntry(
'@header1',
'TTTTTT' + make_sequence(40),
'+',
make_quality_scores(46),
)
fq_fname = self.create_fq_file([entry])
for read, wbrc, randomer in demultiplex._extract(fq_fname,
barcodes,
mismatches=0,
minimum_length=15):
self.assertEqual(wbrc, 'nomatch')
self.assertEqual(randomer, '')
self.assertEqual(read.id, entry.id)
self.assertEqual(read.seq, entry.seq)
self.assertEqual(read.plus, entry.plus)
self.assertEqual(read.qual, entry.qual)
def test_extract_ok_2(self):
# One mismatch, second barcode.
barcodes = demultiplex.prepare_barcodes(self.barcodes5, None)
entry = FastqEntry(
'@header1',
'TTAGTT' + make_sequence(40),
'+',
make_quality_scores(46),
)
fq_fname = self.create_fq_file([entry])
for read, wbrc, randomer in demultiplex._extract(fq_fname,
barcodes,
mismatches=1,
minimum_length=15):
self.assertEqual(wbrc, self.barcodes5[1])
self.assertEqual(randomer, 'TTT')
self.assertEqual(read.id, entry.id)
self.assertEqual(read.seq, entry.seq[6:])
self.assertEqual(read.plus, entry.plus)
self.assertEqual(read.qual, entry.qual[6:])
def test_extract_mismatch(self):
# To many mismatches
barcodes = ['NNAAAN', 'NNCCTN', 'NNACGN']
adapter = 'CCCCCC'
data = [
'@header1', 'TTACTT' + adapter + make_sequence(40, rnd_seed=0),
'+',
make_quality_scores(50, rnd_seed=0) + '!J'
]
fq_fname = get_temp_file_name(extension='fq')
fq_file = iCount.files.fastq.FastqFile(fq_fname, 'wt')
fq_file.write(iCount.files.fastq.FastqEntry(*data))
fq_file.close()
for read, exp_id, randomer in demultiplex._extract(fq_fname,
barcodes,
mismatches=0):
self.assertEqual(exp_id, -1)
self.assertEqual(randomer, '')
self.assertEqual(read.id, data[0])
self.assertEqual(read.seq, data[1])
self.assertEqual(read.plus, '+')
self.assertEqual(read.qual, data[3])
def test_barcode3(self):
# One mismatch, second barcode.
barcodes = demultiplex.prepare_barcodes(
self.barcodes5 + [self.barcodes5[2]], self.barcodes3)
barcodes = barcodes[self.barcodes5[2]]['barcodes3']
entry1 = FastqEntry(
'@header1',
make_sequence(40) + 'TTGGG',
'+',
make_quality_scores(45),
)
entry2 = FastqEntry(
'@header2',
make_sequence(40) + 'TCAAA',
'+',
make_quality_scores(45),
)
fq_fname = self.create_fq_file([entry1, entry2])
handle = demultiplex._extract(fq_fname,
barcodes,
mismatches=1,
minimum_length=15)
read1, wbrc, randomer1 = next(handle)
self.assertEqual(wbrc, self.barcodes3[2])
self.assertEqual(randomer1, 'TT')
self.assertEqual(read1.id, entry1.id)
self.assertEqual(read1.seq, entry1.seq[:-5])
self.assertEqual(read1.plus, entry1.plus)
self.assertEqual(read1.qual, entry1.qual[:-5])
read2, wbrc, randomer2 = next(handle)
self.assertEqual(wbrc, self.barcodes3[3])
self.assertEqual(randomer2, 'TC')
self.assertEqual(read2.id, entry2.id)
self.assertEqual(read2.seq, entry2.seq[:-5])
self.assertEqual(read2.plus, entry2.plus)
self.assertEqual(read2.qual, entry2.qual[:-5])
