def test_single_index_with_lanes(self):
"""SampleSheetBarcodes: single index sample sheet with lanes defined
"""
s = SampleSheetBarcodes(self.single_index_with_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["ACAGTG","CTTGTA",
"GCCAAT","GTGAAA"])
# Check barcodes in each lane
self.assertEqual(s.barcodes(1),["CTTGTA","GCCAAT"])
self.assertEqual(s.barcodes(2),["ACAGTG","GTGAAA"])
# Check all samples
self.assertEqual(s.samples(),["EP1","EP2","ES1","ES2"])
# Check samples in each lane
self.assertEqual(s.samples(1),["EP1","ES1"])
self.assertEqual(s.samples(2),["EP2","ES2"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("GCCAAT",1),"ES1")
self.assertEqual(s.lookup_sample("CTTGTA",1),"EP1")
self.assertEqual(s.lookup_sample("ACAGTG",2),"ES2")
self.assertEqual(s.lookup_sample("GTGAAA",2),"EP2")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("ES1",1),"GCCAAT")
self.assertEqual(s.lookup_barcode("EP1",1),"CTTGTA")
self.assertEqual(s.lookup_barcode("ES2",2),"ACAGTG")
self.assertEqual(s.lookup_barcode("EP2",2),"GTGAAA")
def test_dual_index_no_lanes(self):
"""SampleSheetBarcodes: dual index sample sheet with no lanes defined
"""
s = SampleSheetBarcodes(self.dual_index_no_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["AGGCAGAATCTTACGC",
"CGTACTAGTCTTACGC",
"GGACTCCTTCTTACGC",
"TAAGGCGATCTTACGC",
"TAGGCATGTCTTACGC",
"TCCTGAGCTCTTACGC"])
# Check all samples
self.assertEqual(s.samples(),["SW1","SW2","SW3","SW4","SW5","SW6"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("TAAGGCGATCTTACGC"),"SW1")
self.assertEqual(s.lookup_sample("CGTACTAGTCTTACGC"),"SW2")
self.assertEqual(s.lookup_sample("AGGCAGAATCTTACGC"),"SW3")
self.assertEqual(s.lookup_sample("TCCTGAGCTCTTACGC"),"SW4")
self.assertEqual(s.lookup_sample("GGACTCCTTCTTACGC"),"SW5")
self.assertEqual(s.lookup_sample("TAGGCATGTCTTACGC"),"SW6")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("SW1"),"TAAGGCGATCTTACGC")
self.assertEqual(s.lookup_barcode("SW2"),"CGTACTAGTCTTACGC")
self.assertEqual(s.lookup_barcode("SW3"),"AGGCAGAATCTTACGC")
self.assertEqual(s.lookup_barcode("SW4"),"TCCTGAGCTCTTACGC")
self.assertEqual(s.lookup_barcode("SW5"),"GGACTCCTTCTTACGC")
self.assertEqual(s.lookup_barcode("SW6"),"TAGGCATGTCTTACGC")
def test_single_index_with_lanes(self):
"""SampleSheetBarcodes: single index sample sheet with lanes defined
"""
s = SampleSheetBarcodes(self.single_index_with_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["ACAGTG","CTTGTA",
"GCCAAT","GTGAAA"])
# Check barcodes in each lane
self.assertEqual(s.barcodes(1),["CTTGTA","GCCAAT"])
self.assertEqual(s.barcodes(2),["ACAGTG","GTGAAA"])
# Check all samples
self.assertEqual(s.samples(),["EP1","EP2","ES1","ES2"])
# Check samples in each lane
self.assertEqual(s.samples(1),["EP1","ES1"])
self.assertEqual(s.samples(2),["EP2","ES2"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("GCCAAT",1),"ES1")
self.assertEqual(s.lookup_sample("CTTGTA",1),"EP1")
self.assertEqual(s.lookup_sample("ACAGTG",2),"ES2")
self.assertEqual(s.lookup_sample("GTGAAA",2),"EP2")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("ES1",1),"GCCAAT")
self.assertEqual(s.lookup_barcode("EP1",1),"CTTGTA")
self.assertEqual(s.lookup_barcode("ES2",2),"ACAGTG")
self.assertEqual(s.lookup_barcode("EP2",2),"GTGAAA")
def test_dual_index_no_lanes(self):
"""SampleSheetBarcodes: dual index sample sheet with no lanes defined
"""
s = SampleSheetBarcodes(self.dual_index_no_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["AGGCAGAATCTTACGC",
"CGTACTAGTCTTACGC",
"GGACTCCTTCTTACGC",
"TAAGGCGATCTTACGC",
"TAGGCATGTCTTACGC",
"TCCTGAGCTCTTACGC"])
# Check all samples
self.assertEqual(s.samples(),["SW1","SW2","SW3","SW4","SW5","SW6"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("TAAGGCGATCTTACGC"),"SW1")
self.assertEqual(s.lookup_sample("CGTACTAGTCTTACGC"),"SW2")
self.assertEqual(s.lookup_sample("AGGCAGAATCTTACGC"),"SW3")
self.assertEqual(s.lookup_sample("TCCTGAGCTCTTACGC"),"SW4")
self.assertEqual(s.lookup_sample("GGACTCCTTCTTACGC"),"SW5")
self.assertEqual(s.lookup_sample("TAGGCATGTCTTACGC"),"SW6")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("SW1"),"TAAGGCGATCTTACGC")
self.assertEqual(s.lookup_barcode("SW2"),"CGTACTAGTCTTACGC")
self.assertEqual(s.lookup_barcode("SW3"),"AGGCAGAATCTTACGC")
self.assertEqual(s.lookup_barcode("SW4"),"TCCTGAGCTCTTACGC")
self.assertEqual(s.lookup_barcode("SW5"),"GGACTCCTTCTTACGC")
self.assertEqual(s.lookup_barcode("SW6"),"TAGGCATGTCTTACGC")
def test_non_existent_lane_raises_exception(self):
"""SampleSheetBarcodes: request non-existent lane raises KeyError
"""
# Bad lane for sample sheet with lanes
s = SampleSheetBarcodes(self.dual_index_with_lanes)
self.assertRaises(KeyError,s.barcodes,5)
self.assertRaises(KeyError,s.samples,5)
# Any lane for sample sheet with no lanes
s = SampleSheetBarcodes(self.dual_index_no_lanes)
self.assertRaises(KeyError,s.barcodes,1)
self.assertRaises(KeyError,s.samples,1)
def test_dual_index_with_lanes(self):
"""SampleSheetBarcodes: dual index sample sheet with lanes defined
"""
s = SampleSheetBarcodes(self.dual_index_with_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["ACAGTGATTCTTTCCC",
"ACCGATTCGCGCGTAG",
"ATGCTCGTCTCGCATC",
"ATGCTCGTCTCGCATC",
"ATGTCAGATCTTTCCC",
"CAGATCATTCTTTCCC",
"CCAGCAATATCGCGAG",
"CCGCGTAAGCAATAGA",
"CGTGTAGGATGTAACT",
"CGTGTAGGCACAGGAT",
"CGTGTAGGGACCTGTA",
"CGTGTAGGGTTTCAGA",
"GCCAATATTCTTTCCC",
"GGATTCGCTAGTAGCC",
"TACCAGCGCGCTGCTG"])
# Check barcodes in each lane
self.assertEqual(s.barcodes(1),["CGTGTAGGATGTAACT",
"CGTGTAGGCACAGGAT",
"CGTGTAGGGACCTGTA",
"CGTGTAGGGTTTCAGA"])
self.assertEqual(s.barcodes(2),["CAGATCATTCTTTCCC",
"GCCAATATTCTTTCCC"])
self.assertEqual(s.barcodes(3),["ACCGATTCGCGCGTAG",
"ATGCTCGTCTCGCATC",
"CCGCGTAAGCAATAGA",
"GGATTCGCTAGTAGCC",
"TACCAGCGCGCTGCTG"])
self.assertEqual(s.barcodes(4),["ACAGTGATTCTTTCCC",
"ATGCTCGTCTCGCATC",
"ATGTCAGATCTTTCCC",
"CCAGCAATATCGCGAG"])
# Check all samples
self.assertEqual(s.samples(),["AD5","AEx","AEx",
"AT1","AT3","AT4","AT5",
"D3K1","D3K2",
"DI1","DI2","DI3","DI4",
"E11","E12"])
# Check samples in each lane
self.assertEqual(s.samples(1),["DI1","DI2","DI3","DI4"])
self.assertEqual(s.samples(2),["E11","E12"])
self.assertEqual(s.samples(3),["AEx","AT1","AT3","AT4","AT5"])
self.assertEqual(s.samples(4),["AD5","AEx","D3K1","D3K2"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("CGTGTAGGGACCTGTA",1),"DI1")
self.assertEqual(s.lookup_sample("CGTGTAGGATGTAACT",1),"DI2")
self.assertEqual(s.lookup_sample("CGTGTAGGGTTTCAGA",1),"DI3")
self.assertEqual(s.lookup_sample("CGTGTAGGCACAGGAT",1),"DI4")
self.assertEqual(s.lookup_sample("GCCAATATTCTTTCCC",2),"E11")
self.assertEqual(s.lookup_sample("CAGATCATTCTTTCCC",2),"E12")
self.assertEqual(s.lookup_sample("GGATTCGCTAGTAGCC",3),"AT1")
self.assertEqual(s.lookup_sample("TACCAGCGCGCTGCTG",3),"AT3")
self.assertEqual(s.lookup_sample("ACCGATTCGCGCGTAG",3),"AT4")
self.assertEqual(s.lookup_sample("CCGCGTAAGCAATAGA",3),"AT5")
self.assertEqual(s.lookup_sample("ATGCTCGTCTCGCATC",3),"AEx")
self.assertEqual(s.lookup_sample("ATGCTCGTCTCGCATC",4),"AEx")
self.assertEqual(s.lookup_sample("CCAGCAATATCGCGAG",4),"AD5")
self.assertEqual(s.lookup_sample("ACAGTGATTCTTTCCC",4),"D3K1")
self.assertEqual(s.lookup_sample("ATGTCAGATCTTTCCC",4),"D3K2")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("DI1",1),"CGTGTAGGGACCTGTA")
self.assertEqual(s.lookup_barcode("DI2",1),"CGTGTAGGATGTAACT")
self.assertEqual(s.lookup_barcode("DI3",1),"CGTGTAGGGTTTCAGA")
self.assertEqual(s.lookup_barcode("DI4",1),"CGTGTAGGCACAGGAT")
self.assertEqual(s.lookup_barcode("E11",2),"GCCAATATTCTTTCCC")
self.assertEqual(s.lookup_barcode("E12",2),"CAGATCATTCTTTCCC")
self.assertEqual(s.lookup_barcode("AT1",3),"GGATTCGCTAGTAGCC")
self.assertEqual(s.lookup_barcode("AT3",3),"TACCAGCGCGCTGCTG")
self.assertEqual(s.lookup_barcode("AT4",3),"ACCGATTCGCGCGTAG")
self.assertEqual(s.lookup_barcode("AT5",3),"CCGCGTAAGCAATAGA")
self.assertEqual(s.lookup_barcode("AEx",3),"ATGCTCGTCTCGCATC")
self.assertEqual(s.lookup_barcode("AEx",4),"ATGCTCGTCTCGCATC")
self.assertEqual(s.lookup_barcode("AD5",4),"CCAGCAATATCGCGAG")
self.assertEqual(s.lookup_barcode("D3K1",4),"ACAGTGATTCTTTCCC")
self.assertEqual(s.lookup_barcode("D3K2",4),"ATGTCAGATCTTTCCC")
def test_dual_index_with_lanes(self):
"""SampleSheetBarcodes: dual index sample sheet with lanes defined
"""
s = SampleSheetBarcodes(self.dual_index_with_lanes)
# Check all barcodes
self.assertEqual(s.barcodes(),["ACAGTGATTCTTTCCC",
"ACCGATTCGCGCGTAG",
"ATGCTCGTCTCGCATC",
"ATGCTCGTCTCGCATC",
"ATGTCAGATCTTTCCC",
"CAGATCATTCTTTCCC",
"CCAGCAATATCGCGAG",
"CCGCGTAAGCAATAGA",
"CGTGTAGGATGTAACT",
"CGTGTAGGCACAGGAT",
"CGTGTAGGGACCTGTA",
"CGTGTAGGGTTTCAGA",
"GCCAATATTCTTTCCC",
"GGATTCGCTAGTAGCC",
"TACCAGCGCGCTGCTG"])
# Check barcodes in each lane
self.assertEqual(s.barcodes(1),["CGTGTAGGATGTAACT",
"CGTGTAGGCACAGGAT",
"CGTGTAGGGACCTGTA",
"CGTGTAGGGTTTCAGA"])
self.assertEqual(s.barcodes(2),["CAGATCATTCTTTCCC",
"GCCAATATTCTTTCCC"])
self.assertEqual(s.barcodes(3),["ACCGATTCGCGCGTAG",
"ATGCTCGTCTCGCATC",
"CCGCGTAAGCAATAGA",
"GGATTCGCTAGTAGCC",
"TACCAGCGCGCTGCTG"])
self.assertEqual(s.barcodes(4),["ACAGTGATTCTTTCCC",
"ATGCTCGTCTCGCATC",
"ATGTCAGATCTTTCCC",
"CCAGCAATATCGCGAG"])
# Check all samples
self.assertEqual(s.samples(),["AD5","AEx","AEx",
"AT1","AT3","AT4","AT5",
"D3K1","D3K2",
"DI1","DI2","DI3","DI4",
"E11","E12"])
# Check samples in each lane
self.assertEqual(s.samples(1),["DI1","DI2","DI3","DI4"])
self.assertEqual(s.samples(2),["E11","E12"])
self.assertEqual(s.samples(3),["AEx","AT1","AT3","AT4","AT5"])
self.assertEqual(s.samples(4),["AD5","AEx","D3K1","D3K2"])
# Look up sample names for barcodes in each lane
self.assertEqual(s.lookup_sample("CGTGTAGGGACCTGTA",1),"DI1")
self.assertEqual(s.lookup_sample("CGTGTAGGATGTAACT",1),"DI2")
self.assertEqual(s.lookup_sample("CGTGTAGGGTTTCAGA",1),"DI3")
self.assertEqual(s.lookup_sample("CGTGTAGGCACAGGAT",1),"DI4")
self.assertEqual(s.lookup_sample("GCCAATATTCTTTCCC",2),"E11")
self.assertEqual(s.lookup_sample("CAGATCATTCTTTCCC",2),"E12")
self.assertEqual(s.lookup_sample("GGATTCGCTAGTAGCC",3),"AT1")
self.assertEqual(s.lookup_sample("TACCAGCGCGCTGCTG",3),"AT3")
self.assertEqual(s.lookup_sample("ACCGATTCGCGCGTAG",3),"AT4")
self.assertEqual(s.lookup_sample("CCGCGTAAGCAATAGA",3),"AT5")
self.assertEqual(s.lookup_sample("ATGCTCGTCTCGCATC",3),"AEx")
self.assertEqual(s.lookup_sample("ATGCTCGTCTCGCATC",4),"AEx")
self.assertEqual(s.lookup_sample("CCAGCAATATCGCGAG",4),"AD5")
self.assertEqual(s.lookup_sample("ACAGTGATTCTTTCCC",4),"D3K1")
self.assertEqual(s.lookup_sample("ATGTCAGATCTTTCCC",4),"D3K2")
# Look up barcode matching sample names in each lane
self.assertEqual(s.lookup_barcode("DI1",1),"CGTGTAGGGACCTGTA")
self.assertEqual(s.lookup_barcode("DI2",1),"CGTGTAGGATGTAACT")
self.assertEqual(s.lookup_barcode("DI3",1),"CGTGTAGGGTTTCAGA")
self.assertEqual(s.lookup_barcode("DI4",1),"CGTGTAGGCACAGGAT")
self.assertEqual(s.lookup_barcode("E11",2),"GCCAATATTCTTTCCC")
self.assertEqual(s.lookup_barcode("E12",2),"CAGATCATTCTTTCCC")
self.assertEqual(s.lookup_barcode("AT1",3),"GGATTCGCTAGTAGCC")
self.assertEqual(s.lookup_barcode("AT3",3),"TACCAGCGCGCTGCTG")
self.assertEqual(s.lookup_barcode("AT4",3),"ACCGATTCGCGCGTAG")
self.assertEqual(s.lookup_barcode("AT5",3),"CCGCGTAAGCAATAGA")
self.assertEqual(s.lookup_barcode("AEx",3),"ATGCTCGTCTCGCATC")
self.assertEqual(s.lookup_barcode("AEx",4),"ATGCTCGTCTCGCATC")
self.assertEqual(s.lookup_barcode("AD5",4),"CCAGCAATATCGCGAG")
self.assertEqual(s.lookup_barcode("D3K1",4),"ACAGTGATTCTTTCCC")
self.assertEqual(s.lookup_barcode("D3K2",4),"ATGTCAGATCTTTCCC")