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 = ('','')