def testHappyCleaning(self): bad_tail = [2] * 5 self.baseline.letter_annotations['phred_quality'][-5:] = bad_tail cleaned = strip.clean_for_illumina_flag(self.baseline) self.assertTrue(same_sequence(cleaned, self.baseline[:-5]), self.inequality_error.format(cleaned, self.baseline))
def testInternalBadReadSkippedByCleaning(self): bad_tail = [2] * 5 self.baseline.letter_annotations['phred_quality'][-5:] = bad_tail self.baseline.letter_annotations['phred_quality'][5:10] = bad_tail self.assertEqual(36, len(strip.clean_for_illumina_flag(self.baseline)))
def testTrivialCleaning(self): cleaned = strip.clean_for_illumina_flag(self.baseline) self.assertTrue(same_sequence(cleaned, self.baseline), self.inequality_error.format(cleaned, self.baseline))