def test_parse_illumina_single_end_read_file_N_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions with N (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_in_seq=False)) expected =[] self.assertEqual(actual,expected) # allow one N in barcode actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_in_seq=False, barcode_max_N=1,seq_max_N=0)) expected =[ ('HWI-6X_9267:1:1:4:390#ACNTCCC','GGANGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual,expected) # allow one N in barcode actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_in_seq=False, barcode_max_N=0,seq_max_N=1)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGCC'+\ 'CCCNCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual,expected) # allow one N in barcode and one N in seq actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_in_seq=False, barcode_max_N=1,seq_max_N=1)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGCC'+\ 'CCCNCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACNTCCC','GGANGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual,expected)
def test_parse_illumina_single_end_read_file_N_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions with N (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True)) expected = [] self.assertEqual(actual, expected) # allow one N in barcode actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_max_N=1,seq_max_N=0)) expected =[ ('HWI-6X_9267:1:1:4:390#ACNTCCC','GGANGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual, expected) # allow one N in barcode actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_max_N=0,seq_max_N=1)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGCC'+\ 'CCCNCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual, expected) # allow one N in barcode and one N in seq actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True,barcode_max_N=1,seq_max_N=1)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGCC'+\ 'CCCNCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACNTCCC','GGANGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual, expected)
def test_parse_illumina_single_end_read_file_N_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions with N (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True)) expected = [] self.assertEqual(actual, expected)
def test_parse_illumina_single_end_read_file_N_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions with N (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2_N,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True)) expected =[] self.assertEqual(actual,expected)
def test_parse_illumina_single_end_read_file_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions as expected (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGG'+\ 'GGGGCCCCCCCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual, expected)
def test_parse_illumina_single_end_read_file_no_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions as expected (+ strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read1,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=False,rev_comp_barcode=True)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\ 'CCCCCCCCCCCCCCCCCCCCCCCC',\ 'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaa'+\ 'aaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\ 'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\ 'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAA',\ 'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual, expected)
def test_parse_illumina_single_end_read_file_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions as expected (- strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read2,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=True,rev_comp_barcode=True)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'GGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGG'+\ 'GGGGCCCCCCCCCCCTTTTTTTTAAAA',\ 'cccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbbbba'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA'+\ 'CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',\ 'bbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbb'+\ 'bbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual,expected)
def test_parse_illumina_single_end_read_file_no_revComp(self): """parse_illumina_single_end_read_file: single end read parsing functions as expected (+ strand) """ actual = list(parse_illumina_single_end_read_file(illumina_read1,barcode_length=6,\ max_bad_run_length=0,quality_threshold=1e-5,min_per_read_length=70, rev_comp=False,rev_comp_barcode=True)) expected =[ ('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\ 'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\ 'CCCCCCCCCCCCCCCCCCCCCCCC',\ 'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaa'+\ 'aaaaaaaaaaaaaaaaaaaaaaaa'),\ ('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\ 'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\ 'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAA',\ 'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\ 'aaaaaaaaaaaaaaaaaaaaaaaaaaaa')] self.assertEqual(actual,expected)