def test_analyse_with_no_counts(self):
"""BarcodeCounter: perform analysis for zero counts
"""
bc = BarcodeCounter()
analysis = bc.analyse()
self.assertEqual(analysis.cutoff, None)
self.assertEqual(analysis.mismatches, 0)
self.assertEqual(analysis.total_reads, 0)
self.assertEqual(analysis.coverage, 0)
self.assertEqual(analysis.barcodes, [])
def test_report_barcodes_for_no_counts(self):
"""report_barcodes: check output when there are no counts
"""
bc = BarcodeCounter()
analysis = bc.analyse()
reporter = report_barcodes(bc)
# Check content
self.assertEqual(
str(reporter), """Barcode analysis for all lanes
==============================
* No mismatches were allowed (exact matches only)
No barcodes counted""")
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 count_barcodes(fastqs):
"""
Count the barcodes from multiple fastqs
"""
print "Reading in %s fastq%s" % (len(fastqs),
('' if len(fastqs) == 1 else 's'))
counts = BarcodeCounter()
for fq in fastqs:
print "%s" % os.path.basename(fq)
for r in FastqIterator(fq):
seq = r.seqid.index_sequence
lane = int(r.seqid.flowcell_lane)
counts.count_barcode(seq, lane)
return counts
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_report_barcodes(self):
"""report_barcodes: check output for mismatches and sample sheet
"""
# Create sample sheet
sample_sheet_file = self._make_file(
"SampleSheet.csv", """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
""")
# Set up barcode counts
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("CATGCGCGGTA", lane=1, incr=8532)
bc.count_barcode("GATGCGCGGTA", lane=1, incr=5321)
bc.count_barcode("GCTGCGCGGTA", lane=1, incr=7853)
bc.count_barcode("GCTGCGCGGTC", lane=1, incr=325394)
analysis = bc.analyse(lane=1,
mismatches=2,
sample_sheet=sample_sheet_file)
##"CATGCGCGGTA","TATGCGCGGTA","GATGCGCGGTA","GCTGCGCGGTA" = 307008
##"GCTGCGCGGTC" = 325394
self.assertEqual(analysis.cutoff, None)
self.assertEqual(analysis.mismatches, 2)
self.assertEqual(analysis.total_reads, 632402)
self.assertEqual(analysis.coverage, 632402)
self.assertEqual(analysis.barcodes, ["GCTGCGCGGTC", "CATGCGCGGTA"])
self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads, 325394)
self.assertEqual(analysis.counts["CATGCGCGGTA"].reads, 307008)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample, "SMPL2")
self.assertEqual(analysis.counts["CATGCGCGGTA"].sample, "SMPL1")
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences, 1)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences, 4)
# Create report
reporter = report_barcodes(bc,
lane=1,
mismatches=2,
sample_sheet=sample_sheet_file)
# Check content
self.assertEqual(
str(reporter), """Barcode analysis for lane #1
============================
* Barcodes have been grouped by allowing 2 mismatches
#Rank Index Sample N_seqs N_reads %reads (%Total_reads)
1 GCTGCGCGGTC SMPL2 1 325394 51.5% (51.5%)
2 CATGCGCGGTA SMPL1 4 307008 48.5% (100.0%)""")
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_write_counts_file(self):
"""BarcodeCounter: write counts to a file
"""
# Write a file
self._make_working_dir()
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)
bc.count_barcode("ACCCTNCGGTA", lane=3, incr=312)
bc.count_barcode("ACCTTATGCGC", lane=3, incr=248)
counts_file = os.path.join(self.wd, "out.counts")
bc.write(counts_file)
expected_contents = """#Lane Rank Sequence Count
1 1 TATGCGCGGTA 285302
1 2 TATGCGCGGTG 532
1 3 ACCTACCGGTA 315
1 4 CCCTTATGCGA 22
2 1 ACCTAGCGGTA 477
2 2 ACCTCTATGCT 368
3 1 ACCCTNCGGTA 312
3 2 ACCTTATGCGC 248
"""
self.assertTrue(os.path.exists(counts_file))
self.assertEqual(open(counts_file, 'r').read(), expected_contents)
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)
def test_analyse_groups_with_sample_sheet(self):
"""BarcodeCounter: perform analysis with grouping and samplesheet
"""
# Create sample sheet
sample_sheet_file = self._make_file(
"SampleSheet.csv", """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
2,SMPL3,,,,A005,ACAGTGCGGTA,,
2,SMPL4,,,,A019,GTGAAACGGTC,,
""")
# Set up barcode counts
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("CATGCGCGGTA", lane=1, incr=8532)
bc.count_barcode("GATGCGCGGTA", lane=1, incr=5321)
bc.count_barcode("GCTGCGCGGTA", lane=1, incr=7853)
bc.count_barcode("GCTGCGCGGTC", lane=1, incr=325394)
analysis = bc.analyse(lane=1,
mismatches=2,
sample_sheet=sample_sheet_file)
##"CATGCGCGGTA","TATGCGCGGTA","GATGCGCGGTA","GCTGCGCGGTA" = 307008
##"GCTGCGCGGTC" = 325394
self.assertEqual(analysis.cutoff, None)
self.assertEqual(analysis.mismatches, 2)
self.assertEqual(analysis.total_reads, 632402)
self.assertEqual(analysis.coverage, 632402)
self.assertEqual(analysis.barcodes, ["GCTGCGCGGTC", "CATGCGCGGTA"])
self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads, 325394)
self.assertEqual(analysis.counts["CATGCGCGGTA"].reads, 307008)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample, "SMPL2")
self.assertEqual(analysis.counts["CATGCGCGGTA"].sample, "SMPL1")
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences, 1)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences, 4)
def test_analyse_groups(self):
"""BarcodeCounter: perform analysis with grouping
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("CATGCGCGGTA", lane=1, incr=8532)
bc.count_barcode("GATGCGCGGTA", lane=1, incr=5321)
bc.count_barcode("GCTGCGCGGTA", lane=1, incr=7853)
bc.count_barcode("GCTGCGCGGTC", lane=1, incr=325394)
analysis = bc.analyse(lane=1, mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
self.assertEqual(analysis.cutoff, None)
self.assertEqual(analysis.mismatches, 1)
self.assertEqual(analysis.total_reads, 632402)
self.assertEqual(analysis.coverage, 632402)
self.assertEqual(analysis.barcodes, ["GCTGCGCGGTC", "TATGCGCGGTA"])
self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads, 333247)
self.assertEqual(analysis.counts["TATGCGCGGTA"].reads, 299155)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample, None)
self.assertEqual(analysis.counts["TATGCGCGGTA"].sample, None)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences, 2)
self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences, 3)
def test_analyse_with_cutoff(self):
"""BarcodeCounter: perform analysis with cutoff
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("CATGCGCGGTA", lane=1, incr=8532)
bc.count_barcode("GATGCGCGGTA", lane=1, incr=5321)
bc.count_barcode("GCTGCGCGGTA", lane=1, incr=7853)
bc.count_barcode("GCTGCGCGGTC", lane=1, incr=325394)
analysis = bc.analyse(lane=1, cutoff=0.013)
self.assertEqual(analysis.cutoff, 0.013)
self.assertEqual(analysis.mismatches, 0)
self.assertEqual(analysis.total_reads, 632402)
self.assertEqual(analysis.coverage, 619228)
self.assertEqual(analysis.barcodes,
["GCTGCGCGGTC", "TATGCGCGGTA", "CATGCGCGGTA"])
self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads, 325394)
self.assertEqual(analysis.counts["TATGCGCGGTA"].reads, 285302)
self.assertEqual(analysis.counts["CATGCGCGGTA"].reads, 8532)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample, None)
self.assertEqual(analysis.counts["TATGCGCGGTA"].sample, None)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sample, None)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences, 1)
self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences, 1)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences, 1)
def test_group(self):
"""BarcodeCounter: check grouping of barcode sequences
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA", lane=1, incr=285302)
bc.count_barcode("CATGCGCGGTA", lane=1, incr=8532)
bc.count_barcode("GATGCGCGGTA", lane=1, incr=5321)
bc.count_barcode("GCTGCGCGGTA", lane=1, incr=7853)
bc.count_barcode("GCTGCGCGGTC", lane=1, incr=325394)
bc.count_barcode("GTCACGCGGTA", lane=2, incr=296201)
bc.count_barcode("GTCACGCGGTT", lane=2, incr=2853)
bc.count_barcode("GTCACGCTGTT", lane=2, incr=278539)
## 2 mismatches across all lanes
groups = bc.group(None, mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups), 3)
self.assertEqual(groups[0].reference, "GTCACGCGGTA")
self.assertEqual(groups[0].sequences,
["GTCACGCGGTA", "GTCACGCTGTT", "GTCACGCGGTT"])
self.assertEqual(groups[0].counts, 577593)
self.assertEqual(groups[1].reference, "GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,
["GCTGCGCGGTC", "GCTGCGCGGTA", "GATGCGCGGTA"])
self.assertEqual(groups[1].counts, 338568)
self.assertEqual(groups[2].reference, "TATGCGCGGTA")
self.assertEqual(groups[2].sequences, ["TATGCGCGGTA", "CATGCGCGGTA"])
self.assertEqual(groups[2].counts, 293834)
## 1 mismatch across all lanes
groups = bc.group(None, mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
##"GTCACGCGGTA","GTCACGCGGTT" = 299054
##"GTCACGCTGTT" = 278539
self.assertEqual(len(groups), 4)
self.assertEqual(groups[0].reference, "GCTGCGCGGTC")
self.assertEqual(groups[0].sequences, ["GCTGCGCGGTC", "GCTGCGCGGTA"])
self.assertEqual(groups[0].counts, 333247)
self.assertEqual(groups[1].reference, "TATGCGCGGTA")
self.assertEqual(groups[1].sequences,
["TATGCGCGGTA", "CATGCGCGGTA", "GATGCGCGGTA"])
self.assertEqual(groups[1].counts, 299155)
self.assertEqual(groups[2].reference, "GTCACGCGGTA")
self.assertEqual(groups[2].sequences, ["GTCACGCGGTA", "GTCACGCGGTT"])
self.assertEqual(groups[2].counts, 299054)
self.assertEqual(groups[3].reference, "GTCACGCTGTT")
self.assertEqual(groups[3].sequences, [
"GTCACGCTGTT",
])
self.assertEqual(groups[3].counts, 278539)
## 1 mismatch in lane 1
groups = bc.group(1, mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
self.assertEqual(len(groups), 2)
self.assertEqual(groups[0].reference, "GCTGCGCGGTC")
self.assertEqual(groups[0].sequences, ["GCTGCGCGGTC", "GCTGCGCGGTA"])
self.assertEqual(groups[0].counts, 333247)
self.assertEqual(groups[1].reference, "TATGCGCGGTA")
self.assertEqual(groups[1].sequences,
["TATGCGCGGTA", "CATGCGCGGTA", "GATGCGCGGTA"])
self.assertEqual(groups[1].counts, 299155)
## 2 mismatches across all lanes
groups = bc.group(None, mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups), 3)
self.assertEqual(groups[0].reference, "GTCACGCGGTA")
self.assertEqual(groups[0].sequences,
["GTCACGCGGTA", "GTCACGCTGTT", "GTCACGCGGTT"])
self.assertEqual(groups[0].counts, 577593)
self.assertEqual(groups[1].reference, "GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,
["GCTGCGCGGTC", "GCTGCGCGGTA", "GATGCGCGGTA"])
self.assertEqual(groups[1].counts, 338568)
self.assertEqual(groups[2].reference, "TATGCGCGGTA")
self.assertEqual(groups[2].sequences, ["TATGCGCGGTA", "CATGCGCGGTA"])
self.assertEqual(groups[2].counts, 293834)
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",
])
# Report name and version
p.print_version()
# Process command line
opts, args = p.parse_args()
# Anything to do?
if len(args) == 0:
if opts.use_counts:
p.error("Needs at least one barcode counts file")
else:
p.error("Needs at least one FASTQ file, or a bcl2fastq directory")
# Set default return value
retval = 0
# Determine mode
if opts.use_counts:
# Read counts from counts file(s)
counts = BarcodeCounter(*args)
elif len(args) == 1 and os.path.isdir(args[0]):
# Generate counts from bcl2fastq output
counts = count_barcodes_bcl2fastq(args[0])
else:
# Generate counts from fastq files
counts = count_barcodes(args)
# Determine subset of lanes to examine
if opts.lanes is not None:
lanes = parse_lanes(opts.lanes)
else:
lanes = counts.lanes
# Deal with cutoff
if opts.cutoff == 0.0:
cutoff = None
else:
