def test_read_qual_score_filter(self):
"""read_qual_score_filter: functions as expected
"""
actual = read_qual_score_filter('ACGTACGTA','aa``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTA', 'aa``ba^``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','Ba``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('', '')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aB``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('A', 'a')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``ba^`B',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGT', 'aa``ba^`')
self.assertEqual(actual, expected)
actual = read_qual_score_filter(\
'','',max_run_length=0,threshold=1e-5)
expected = ('', '')
self.assertEqual(actual, expected)
actual = read_qual_score_filter(\
'ACGTACGTANNNNNNNNNAAAAAAAACCCCCCCC',\
'aa``ba^``bbbbbbbbbbbbbbbbbbbbbbbbb',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTANNNNNNNNNAAAAAAAACCCCCCCC',\
'aa``ba^``bbbbbbbbbbbbbbbbbbbbbbbbb')
def test_read_qual_score_filter(self):
"""read_qual_score_filter: functions as expected
"""
actual = read_qual_score_filter('ACGTACGTA','aa``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTA','aa``ba^``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','Ba``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('','')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aB``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('A','a')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``ba^`B',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGT','aa``ba^`')
self.assertEqual(actual,expected)
actual = read_qual_score_filter(\
'','',max_run_length=0,threshold=1e-5)
expected = ('','')
self.assertEqual(actual,expected)
actual = read_qual_score_filter(\
'ACGTACGTANNNNNNNNNAAAAAAAACCCCCCCC',\
'aa``ba^``bbbbbbbbbbbbbbbbbbbbbbbbb',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTANNNNNNNNNAAAAAAAACCCCCCCC',\
'aa``ba^``bbbbbbbbbbbbbbbbbbbbbbbbb')
def test_read_qual_score_filter_alt_bad_run_length(self):
"""read_qual_score_filter: functions as expected w alt max_run_length
"""
actual = read_qual_score_filter('ACGTACGTA','aa``Ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGT', 'aa``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','BBBBBBBBB',\
max_run_length=0,threshold=1e-5)
expected = ('', '')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','Ba``Ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('', '')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``Ba^``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGTACGTA', 'aa``Ba^``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``B^B``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGTACGTA', 'aa``B^B``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``BB^``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGT', 'aa``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``BB^``',\
max_run_length=2,threshold=1e-5)
expected = ('ACGTACGTA', 'aa``BB^``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','BBBBBBBBB',\
max_run_length=9,threshold=1e-5)
expected = ('ACGTACGTA', 'BBBBBBBBB')
self.assertEqual(actual, expected)
def test_read_qual_score_filter_alt_bad_run_length(self):
"""read_qual_score_filter: functions as expected w alt max_run_length
"""
actual = read_qual_score_filter('ACGTACGTA','aa``Ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGT','aa``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','BBBBBBBBB',\
max_run_length=0,threshold=1e-5)
expected = ('','')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','Ba``Ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('','')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``Ba^``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGTACGTA','aa``Ba^``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``B^B``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGTACGTA','aa``B^B``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``BB^``',\
max_run_length=1,threshold=1e-5)
expected = ('ACGT','aa``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``BB^``',\
max_run_length=2,threshold=1e-5)
expected = ('ACGTACGTA','aa``BB^``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','BBBBBBBBB',\
max_run_length=9,threshold=1e-5)
expected = ('ACGTACGTA','BBBBBBBBB')
self.assertEqual(actual,expected)
def test_read_qual_score_filter_alt_p_threshold(self):
"""read_qual_score_filter: functions as expected w alt p threshold
"""
actual = read_qual_score_filter('ACGTACGTA','aa``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTA', 'aa``ba^``')
self.assertEqual(actual, expected)
# change threshold to filter/not filter on C
actual = read_qual_score_filter('ACGTACGTA','aa``Ca^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGT', 'aa``')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','aa``Ca^``',\
max_run_length=0,threshold=1e-2)
expected = ('ACGTACGTA', 'aa``Ca^``')
self.assertEqual(actual, expected)
# Lowest prob value is 1e-62 associated with ~
actual = read_qual_score_filter('ACGTACGTA','~~~~~~~~~',\
max_run_length=0,threshold=1e-62)
expected = ('ACGTACGTA', '~~~~~~~~~')
self.assertEqual(actual, expected)
actual = read_qual_score_filter('ACGTACGTA','~~~~~~~~~',\
max_run_length=0,threshold=1e-63)
expected = ('', '')
self.assertEqual(actual, expected)
# Highest prob value is 1. associated with @
actual = read_qual_score_filter('ACGTACGTA','@@@@@@@@@',\
max_run_length=0,threshold=1.)
expected = ('ACGTACGTA', '@@@@@@@@@')
actual = read_qual_score_filter('ACGTACGTA','@@@@@@@@@',\
max_run_length=0,threshold=0.1)
expected = ('', '')
def test_read_qual_score_filter_alt_p_threshold(self):
"""read_qual_score_filter: functions as expected w alt p threshold
"""
actual = read_qual_score_filter('ACGTACGTA','aa``ba^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGTACGTA','aa``ba^``')
self.assertEqual(actual,expected)
# change threshold to filter/not filter on C
actual = read_qual_score_filter('ACGTACGTA','aa``Ca^``',\
max_run_length=0,threshold=1e-5)
expected = ('ACGT','aa``')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','aa``Ca^``',\
max_run_length=0,threshold=1e-2)
expected = ('ACGTACGTA','aa``Ca^``')
self.assertEqual(actual,expected)
# Lowest prob value is 1e-62 associated with ~
actual = read_qual_score_filter('ACGTACGTA','~~~~~~~~~',\
max_run_length=0,threshold=1e-62)
expected = ('ACGTACGTA','~~~~~~~~~')
self.assertEqual(actual,expected)
actual = read_qual_score_filter('ACGTACGTA','~~~~~~~~~',\
max_run_length=0,threshold=1e-63)
expected = ('','')
self.assertEqual(actual,expected)
# Highest prob value is 1. associated with @
actual = read_qual_score_filter('ACGTACGTA','@@@@@@@@@',\
max_run_length=0,threshold=1.)
expected = ('ACGTACGTA','@@@@@@@@@')
actual = read_qual_score_filter('ACGTACGTA','@@@@@@@@@',\
max_run_length=0,threshold=0.1)
expected = ('','')
