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_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 barcodes counted""")
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 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 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_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_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_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_analyse_with_sample_sheet(self):
"""BarcodeCounter: perform analysis with 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,sample_sheet=sample_sheet_file)
self.assertEqual(analysis.cutoff,None)
self.assertEqual(analysis.mismatches,0)
self.assertEqual(analysis.total_reads,632402)
self.assertEqual(analysis.coverage,632402)
self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
"TATGCGCGGTA",
"CATGCGCGGTA",
"GCTGCGCGGTA",
"GATGCGCGGTA"])
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["GCTGCGCGGTA"].reads,7853)
self.assertEqual(analysis.counts["GATGCGCGGTA"].reads,5321)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,"SMPL2")
self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,"SMPL1")
self.assertEqual(analysis.counts["GCTGCGCGGTA"].sample,None)
self.assertEqual(analysis.counts["GATGCGCGGTA"].sample,None)
self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,1)
self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,1)
self.assertEqual(analysis.counts["GCTGCGCGGTA"].sequences,1)
self.assertEqual(analysis.counts["GATGCGCGGTA"].sequences,1)
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_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_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_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_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)
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")
# Determine subset of lanes to examine
if opts.lanes is not None:
lanes = parse_lanes(opts.lanes)
else:
lanes = None
# 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)
# Deal with cutoff
if opts.cutoff == 0.0:
cutoff = None
else:
cutoff = opts.cutoff
# Report the counts
if not opts.no_report:
reporter = Reporter()
if lanes is None:
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)
# 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")
# Determine subset of lanes to examine
lanes = parse_lanes_expression(opts.lanes)
# 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)
# Deal with cutoff
if opts.cutoff == 0.0:
cutoff = None
else:
cutoff = opts.cutoff
# Report the counts
if not opts.no_report:
reporter = Reporter()
if lanes is None:
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_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_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_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_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_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_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_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_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)