def test_read_old_style_counts_file(self):
"""BarcodeCounter: read in data from old-style 3 column '.counts' file
"""
# Read old-style 3 column counts files
self._make_working_dir()
old_style_counts_file = self._make_file(
"old_style.counts", """#Rank Sequence Count
1 TATGCGCGGTA 285302
2 TATGCGCGGTG 532
3 ACCTACCGGTA 315
4 CCCTTATGCGA 22""")
# Read the file
bc = BarcodeCounter(old_style_counts_file)
# Check the contents
self.assertEqual(
bc.barcodes(),
["TATGCGCGGTA", "TATGCGCGGTG", "ACCTACCGGTA", "CCCTTATGCGA"])
# Lanes
self.assertEqual(bc.lanes, [])
# Counts for individual barcodes
self.assertEqual(bc.counts("TATGCGCGGTA"), 285302)
self.assertEqual(bc.counts("TATGCGCGGTG"), 532)
self.assertEqual(bc.counts("ACCTACCGGTA"), 315)
self.assertEqual(bc.counts("CCCTTATGCGA"), 22)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=1), 0)
self.assertEqual(bc.counts_all("TATGCGCGGTA"), 285302)
# Read counts
self.assertEqual(bc.nreads(), 286171)
def test_filter_barcodes(self):
"""BarcodeCounter: check filtering by lane and cutoff
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("TATGCGCGGTG", lane=1, incr=532)
bc.count_barcode("ACCTACCGGTA", lane=1, incr=315)
bc.count_barcode("CCCTTATGCGA", lane=1, incr=22)
bc.count_barcode("ACCTAGCGGTA", lane=2, incr=477)
bc.count_barcode("ACCTCTATGCT", lane=2, incr=368)
self.assertEqual(bc.barcodes(), [
"TATGCGCGGTA", "TATGCGCGGTG", "ACCTAGCGGTA", "ACCTCTATGCT",
"ACCTACCGGTA", "CCCTTATGCGA"
])
# No filtering
self.assertEqual(bc.filter_barcodes(), [
"TATGCGCGGTA", "TATGCGCGGTG", "ACCTAGCGGTA", "ACCTCTATGCT",
"ACCTACCGGTA", "CCCTTATGCGA"
])
# Filter by lane
self.assertEqual(
bc.filter_barcodes(lane=1),
["TATGCGCGGTA", "TATGCGCGGTG", "ACCTACCGGTA", "CCCTTATGCGA"]),
self.assertEqual(bc.filter_barcodes(lane=2),
["ACCTAGCGGTA", "ACCTCTATGCT"])
# Filter by cutoff
self.assertEqual(bc.filter_barcodes(cutoff=0.5), [
"TATGCGCGGTA",
])
self.assertEqual(bc.filter_barcodes(cutoff=0.0015, lane=1),
["TATGCGCGGTA", "TATGCGCGGTG"])
self.assertEqual(bc.filter_barcodes(cutoff=0.5, lane=2), [
"ACCTAGCGGTA",
])
def test_empty_counter(self):
"""BarcodeCounter: check empty counter
"""
# Initialise counter object
bc = BarcodeCounter()
self.assertEqual(bc.barcodes(), [])
self.assertEqual(bc.lanes, [])
self.assertEqual(bc.filter_barcodes(), [])
self.assertEqual(bc.counts("AGGCAGAATCTTACGC"), 0)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC", lane=1), 0)
self.assertEqual(bc.counts_all("AGGCAGAATCTTACGC"), 0)
self.assertEqual(bc.nreads(), 0)
self.assertEqual(bc.nreads(1), 0)
def test_count_fastq_sequences(self):
"""BarcodeCounter: count barcode sequences
"""
# Initialise counter object
bc = BarcodeCounter()
# Populate with sequences
for r, incr in (((1, "AGGCAGAATCTTACGC"),
102), ((1, "TCCTGAGCTCTTACGC"),
10), ((1, "ACAGTGATTCTTTCCC"),
3), ((1, "ATGCTCGTCTCGCATC"),
1), ((2, "CGTACTAGTCTTACGC"), 95),
((2, "ATGTCAGATCTTTCCC"),
29), ((2, "AGGCAGAATCTTACGC"),
12), ((2, "CAGATCATTCTTTCCC"),
6), ((3, "GGACTCCTTCTTACGC"),
75), ((3, "ACCGATTCGCGCGTAG"), 74),
((3, "CCAGCAATATCGCGAG"), 2), ((3, "CCGCGTAAGCAATAGA"),
1)):
lane, seq = r
for i in xrange(incr):
bc.count_barcode(seq, lane=lane)
# Check contents
self.assertEqual(bc.barcodes(), [
"AGGCAGAATCTTACGC", "CGTACTAGTCTTACGC", "GGACTCCTTCTTACGC",
"ACCGATTCGCGCGTAG", "ATGTCAGATCTTTCCC", "TCCTGAGCTCTTACGC",
"CAGATCATTCTTTCCC", "ACAGTGATTCTTTCCC", "CCAGCAATATCGCGAG",
"ATGCTCGTCTCGCATC", "CCGCGTAAGCAATAGA"
])
# Lanes
self.assertEqual(bc.lanes, [1, 2, 3])
# Counts for individual barcodes
self.assertEqual(bc.counts("AGGCAGAATCTTACGC"), 114)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC", lane=1), 102)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC", lane=2), 12)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC", lane=3), 0)
self.assertEqual(bc.counts_all("AGGCAGAATCTTACGC"), 114)
self.assertEqual(bc.counts("CCGCGTAAGCAATAGA"), 1)
self.assertEqual(bc.counts("CCGCGTAAGCAATAGA", lane=1), 0)
self.assertEqual(bc.counts("CCGCGTAAGCAATAGA", lane=2), 0)
self.assertEqual(bc.counts("CCGCGTAAGCAATAGA", lane=3), 1)
self.assertEqual(bc.counts_all("CCGCGTAAGCAATAGA"), 1)
# Read counts
self.assertEqual(bc.nreads(), 410)
self.assertEqual(bc.nreads(1), 116)
self.assertEqual(bc.nreads(2), 142)
self.assertEqual(bc.nreads(3), 152)
# Lengths
self.assertEqual(bc.barcode_lengths(), [16])
self.assertEqual(bc.barcode_lengths(1), [16])
self.assertEqual(bc.barcode_lengths(2), [16])
self.assertEqual(bc.barcode_lengths(3), [16])
def test_read_multiple_counts_file(self):
"""BarcodeCounter: read in data from multiple '.counts' files
"""
# Read multiple counts files
counts_lane1 = self._make_file(
"lane1.counts", """#Lane Rank Sequence Count
1 1 TATGCGCGGTA 285302
1 2 TATGCGCGGTG 532
1 3 ACCTACCGGTA 315
1 4 CCCTTATGCGA 22""")
counts_lane2 = self._make_file(
"lane2.counts", """#Lane Rank Sequence Count
2 1 ACCTAGCGGTA 477
2 2 ACCTCTATGCT 368""")
counts_lane3 = self._make_file(
"lane3.counts", """#Lane Rank Sequence Count
3 1 ACCCTNCGGTA 312
3 2 ACCTTATGCGC 248""")
# Read the file
bc = BarcodeCounter(counts_lane1, counts_lane2, counts_lane3)
# Check the contents
self.assertEqual(bc.barcodes(), [
"TATGCGCGGTA", "TATGCGCGGTG", "ACCTAGCGGTA", "ACCTCTATGCT",
"ACCTACCGGTA", "ACCCTNCGGTA", "ACCTTATGCGC", "CCCTTATGCGA"
])
# Lanes
self.assertEqual(bc.lanes, [1, 2, 3])
# Counts for individual barcodes
self.assertEqual(bc.counts("TATGCGCGGTA"), 285302)
self.assertEqual(bc.counts("TATGCGCGGTG"), 532)
self.assertEqual(bc.counts("ACCTAGCGGTA"), 477)
self.assertEqual(bc.counts("ACCTCTATGCT"), 368)
self.assertEqual(bc.counts("ACCTACCGGTA"), 315)
self.assertEqual(bc.counts("ACCCTNCGGTA"), 312)
self.assertEqual(bc.counts("ACCTTATGCGC"), 248)
self.assertEqual(bc.counts("CCCTTATGCGA"), 22)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=1), 285302)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=2), 0)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=3), 0)
self.assertEqual(bc.counts_all("TATGCGCGGTA"), 285302)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=1), 0)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=2), 0)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=3), 248)
self.assertEqual(bc.counts_all("ACCTTATGCGC"), 248)
# Read counts
self.assertEqual(bc.nreads(), 287576)
self.assertEqual(bc.nreads(1), 286171)
self.assertEqual(bc.nreads(2), 845)
self.assertEqual(bc.nreads(3), 560)
def test_read_counts_file(self):
"""BarcodeCounter: read in data from '.counts' file
"""
# Read a counts file
counts_file = self._make_file(
"test.counts", """#Lane Rank Sequence Count
1 1 TATGCGCGGTA 285302
1 2 TATGCGCGGTG 532
1 3 ACCTACCGGTA 315
1 4 CCCTTATGCGA 22
2 5 ACCTAGCGGTA 477
2 6 ACCTCTATGCT 368
3 7 ACCCTNCGGTA 312
3 8 ACCTTATGCGC 248""")
# Read the file
bc = BarcodeCounter(counts_file)
# Check the contents
self.assertEqual(bc.barcodes(), [
"TATGCGCGGTA", "TATGCGCGGTG", "ACCTAGCGGTA", "ACCTCTATGCT",
"ACCTACCGGTA", "ACCCTNCGGTA", "ACCTTATGCGC", "CCCTTATGCGA"
])
# Lanes
self.assertEqual(bc.lanes, [1, 2, 3])
# Counts for individual barcodes
self.assertEqual(bc.counts("TATGCGCGGTA"), 285302)
self.assertEqual(bc.counts("TATGCGCGGTG"), 532)
self.assertEqual(bc.counts("ACCTAGCGGTA"), 477)
self.assertEqual(bc.counts("ACCTCTATGCT"), 368)
self.assertEqual(bc.counts("ACCTACCGGTA"), 315)
self.assertEqual(bc.counts("ACCCTNCGGTA"), 312)
self.assertEqual(bc.counts("ACCTTATGCGC"), 248)
self.assertEqual(bc.counts("CCCTTATGCGA"), 22)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=1), 285302)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=2), 0)
self.assertEqual(bc.counts("TATGCGCGGTA", lane=3), 0)
self.assertEqual(bc.counts_all("TATGCGCGGTA"), 285302)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=1), 0)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=2), 0)
self.assertEqual(bc.counts("ACCTTATGCGC", lane=3), 248)
self.assertEqual(bc.counts_all("ACCTTATGCGC"), 248)
# Read counts
self.assertEqual(bc.nreads(), 287576)
self.assertEqual(bc.nreads(1), 286171)
self.assertEqual(bc.nreads(2), 845)
self.assertEqual(bc.nreads(3), 560)