def test_parse_illumina_paired_end_read_files_error(self):
"""parse_illumina_paired_end_read_files: detects mis-matched lines """
reversed_illumina_read_lines1 = \
[self.illumina_read1[1],self.illumina_read1[0]]
record_iter = parse_illumina_paired_end_read_files(\
reversed_illumina_read_lines1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75)
self.assertRaises(IlluminaParseError, list, record_iter)
reversed_illumina_read_lines2 = \
[self.illumina_read2[1],self.illumina_read2[0]]
record_iter = parse_illumina_paired_end_read_files(\
illumina_read1,reversed_illumina_read_lines2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75)
self.assertRaises(IlluminaParseError, list, record_iter)
# no error if reversed-order files are passed
list(parse_illumina_paired_end_read_files(\
reversed_illumina_read_lines1,reversed_illumina_read_lines2,\
barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75))
def test_parse_illumina_paired_end_read_files_error(self):
"""parse_illumina_paired_end_read_files: detects mis-matched lines """
reversed_illumina_read_lines1 = \
[self.illumina_read1[1],self.illumina_read1[0]]
record_iter = parse_illumina_paired_end_read_files(\
reversed_illumina_read_lines1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75)
self.assertRaises(IlluminaParseError,list,record_iter)
reversed_illumina_read_lines2 = \
[self.illumina_read2[1],self.illumina_read2[0]]
record_iter = parse_illumina_paired_end_read_files(\
illumina_read1,reversed_illumina_read_lines2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75)
self.assertRaises(IlluminaParseError,list,record_iter)
# no error if reversed-order files are passed
list(parse_illumina_paired_end_read_files(\
reversed_illumina_read_lines1,reversed_illumina_read_lines2,\
barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75))
def test_parse_illumina_paired_end_read_files_N(self):
"""parse_illumina_paired_end_read_files: functions as expected with N chars"""
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual,expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual,expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual,expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,barcode_max_N=1))
self.assertEqual(len(actual),1)
# one sequence discarded due to barcode N, other due to 2 sequence Ns
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,seq_max_N=1))
self.assertEqual(len(actual),0)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,barcode_max_N=1,seq_max_N=2))
self.assertEqual(len(actual),2)
def test_parse_illumina_paired_end_read_files_N(self):
"""parse_illumina_paired_end_read_files: functions as expected with N chars"""
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual, expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual, expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = []
self.assertEqual(actual, expected)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,barcode_max_N=1))
self.assertEqual(len(actual), 1)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,seq_max_N=1))
self.assertEqual(len(actual), 1)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1_N,illumina_read2_N,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70,barcode_max_N=1,seq_max_N=1))
self.assertEqual(len(actual), 2)
def test_parse_illumina_paired_end_read_files(self):
"""parse_illumina_paired_end_read_files: functions as expected """
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = [
('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\
'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCCCCCCCCCCCGGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGG'+\
'GGGGGGCCCCCCCCCCCTTTTTTTTAAAA',\
'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaacccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\
('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAACGTACGTACGT'+\
'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'+\
'GTACGTACGTACGTACGTACGTACGT',\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbb'+\
'bbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')]
self.assertEqual(actual, expected)
# alt min_per_read_length
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75))
expected = [
('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAACGTACGTACGT'+\
'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'+\
'GTACGTACGTACGTACGTACGTACGT',\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbb'+\
'bbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')]
self.assertEqual(actual, expected)
# alt quality_threshold (just checking number of results
# to be sure that alt value is passed through)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual), 0)
# alt max_bad_run_length (just checking number of results
# to be sure that alt value is passed through)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual), 0)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=150,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual), 2)
def test_parse_illumina_paired_end_read_files(self):
"""parse_illumina_paired_end_read_files: functions as expected """
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=70))
expected = [
('HWI-6X_9267:1:1:4:1699#ACCACCC','GGTGGT',\
'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCCCCCCCCCCCGGTTTTTTTTTAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGG'+\
'GGGGGGCCCCCCCCCCCTTTTTTTTAAAA',\
'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaacccccccccccccccccbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'),\
('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAACGTACGTACGT'+\
'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'+\
'GTACGTACGTACGTACGTACGTACGT',\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbb'+\
'bbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')]
self.assertEqual(actual,expected)
# alt min_per_read_length
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-5,
min_per_read_length=75))
expected = [
('HWI-6X_9267:1:1:4:390#ACCTCCC','GGAGGT',\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAACGTACGTACGT'+\
'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'+\
'GTACGTACGTACGTACGTACGTACGT',\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbb'+\
'bbbbbbaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbb'+\
'bbbbaaaaaaaaaaaaaaaaaaaaaaaaaa')]
self.assertEqual(actual,expected)
# alt quality_threshold (just checking number of results
# to be sure that alt value is passed through)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual),0)
# alt max_bad_run_length (just checking number of results
# to be sure that alt value is passed through)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=0,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual),0)
actual = list(parse_illumina_paired_end_read_files(\
illumina_read1,illumina_read2,barcode_length=6,\
max_bad_run_length=150,rev_comp_barcode=True,quality_threshold=1e-55,
min_per_read_length=75))
self.assertEqual(len(actual),2)
