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_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_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_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_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_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)
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)
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)
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)
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_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",])
