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)
