def test_quality_filter_sequence_pass(self):
"""quality_filter_sequence functions as expected for good read
"""
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
def test_quality_filter_sequence_fail_w_N(self):
"""quality_filter_sequence handles N as expected
"""
# 'N' in sequence causes failure
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTNGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
expected = (2,
"GCACTCACCGCCCGTCACACCACGAAAGTNGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`")
self.assertEqual(actual,expected)
# increasing max N rescues sequence
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTNGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=1,
filter_bad_illumina_qual_digit=True)
expected = (0,
"GCACTCACCGCCCGTCACACCACGAAAGTNGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`")
self.assertEqual(actual,expected)
# truncation of N rescues sequence (sequence is truncated when
# the quality hits B, and the truncated sequence is above the
# length threshold and no longer contains an N)
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTN"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^B`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=50,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
expected = (0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTG",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^")
self.assertEqual(actual,expected)
def test_quality_filter_sequence_fail_w_B(self):
"""quality_filter_sequence handles bad qual score as expected
"""
# early 'B' in sequence causes truncation and too short of a read
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(1,"GCACTCACCGCCCGTCAC","bbbbbbbbbbbbbbbbbb"))
# increasing max_bad_run_length rescues read
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=1,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# changing threshold rescues read
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='A',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# changing min_per_read_length rescues read
header = "990:2:4:11271:5323#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbBbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=5,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,"GCACTCACCGCCCGTCAC","bbbbbbbbbbbbbbbbbb"))
def test_quality_filter_illumina_qual(self):
"""quality_filter_sequence functions as expected with bad illumina qual digit
"""
# header with no qual data passes
header = "990:2:4:11271:5323/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# header with no qual data passes
header = "990:2:4:11271:5323/0"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# header with no qual data passes (old barcode in header format)
header = "HWI-6X_9267:1:1:4:1699#ACCACCC/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# bad qual fails filter
header = "@HWI-ST753_50:6:1101:1138:1965#0/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(3,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# bad qual passes filter if filter turned off
header = "@HWI-ST753_50:6:1101:1138:1965#0/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=False)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
# good qual passes filter
header = "@HWI-ST753_50:6:1101:1138:1965#1/1"
sequence = \
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC"
quality = \
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"
actual = quality_filter_sequence(header,
sequence,
quality,
max_bad_run_length=0,
last_bad_quality_char='B',
min_per_read_length=75,
seq_max_N=0,
filter_bad_illumina_qual_digit=True)
self.assertEqual(actual,(0,
"GCACTCACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGAGATAACCTTTTAGGAGTCAGCTGTC",
"bbbbbbbbbbbbbbbbbbbbbbbbbY``\`bbbbbbbbbbbbb`bbbbab`a`_[ba_aa]b^_bIWTTQ^YR^U`"))
