示例#1
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 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")
示例#2
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 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")
示例#5
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 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)
示例#6
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 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")