def test_barcode_size_diff(self):
barcodes5 = [
'NATAN',
'NNNCAGN',
]
barcodes = demultiplex.prepare_barcodes(barcodes5, None)
index = demultiplex.create_index(barcodes)
expected = {
1: {
'A': {barcodes5[0]}
},
2: {
'T': {barcodes5[0]}
},
3: {
'A': {barcodes5[0]},
'C': {barcodes5[1]},
},
4: {
'A': {barcodes5[1]},
},
5: {
'G': {barcodes5[1]},
},
}
self.assertEqual(index, expected)
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_barcode3(self):
barcodes5 = [
'NATN',
'NNCAN',
'NNCAN',
]
barcodes3 = [
'NNTAG',
'NNGT',
'.',
]
barcodes = demultiplex.prepare_barcodes(barcodes5, barcodes3)
index = demultiplex.create_index(barcodes)
self.assertEqual(
index, {
1: {
'A': {barcodes5[0]}
},
2: {
'T': {barcodes5[0]},
'C': {barcodes5[1]},
},
3: {
'A': {barcodes5[1]},
},
})
index3 = demultiplex.create_index(barcodes['NATN']['barcodes3'])
self.assertEqual(
index3, {
-3: {
'T': {barcodes3[0]},
},
-2: {
'A': {barcodes3[0]},
},
-1: {
'G': {barcodes3[0]},
},
})
index3 = demultiplex.create_index(barcodes['NNCAN']['barcodes3'])
self.assertEqual(index3, {
-2: {
'G': {barcodes3[1]},
},
-1: {
'T': {barcodes3[1]},
},
})
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_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])
def test_create_index_simple(self):
barcodes5 = [
'NNAAAN',
'NNACTN',
'NNACGN',
]
barcodes = demultiplex.prepare_barcodes(barcodes5, None)
index = demultiplex.create_index(barcodes)
expected = {
2: {
'A': {barcodes5[0], barcodes5[1], barcodes5[2]}
},
3: {
'A': {barcodes5[0]},
'C': {barcodes5[1], barcodes5[2]},
},
4: {
'A': {barcodes5[0]},
'T': {barcodes5[1]},
'G': {barcodes5[2]},
},
}
self.assertEqual(index, expected)
