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_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_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_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_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)