def testTrivialProcessSequences(self): processed = strip.processed_sequences(self.primer, [self.baseline], self.min_sequence_len, self.min_primer_match, self.max_primer_offset).next() self.assertTrue(same_sequence(processed, self.baseline), self.inequality_error.format(processed, self.baseline))
def testTooSmallAfterCleaning(self): bad_tail = [2] * (len(self.baseline) - 16) self.baseline.letter_annotations['phred_quality'][16:] = bad_tail processed = strip.processed_sequences(self.primer, [self.baseline], self.min_sequence_len, self.min_primer_match) self.assertEqual([], list(processed))
def testTrimAndClean(self): s = self.baseline[:28] + self.primer_seq[:12] s.letter_annotations['phred_quality'][-20:] = [2] * 20 processed = strip.processed_sequences(self.primer, [s], self.min_sequence_len, self.min_primer_match).next() self.assertTrue(same_sequence(processed, s[:20]), self.inequality_error.format(processed, s[:20]))
def testTooSmallAfterTrimming(self): l = len(self.primer_seq) + 15 s = self.baseline[:15] + self.primer_seq + self.baseline[l:] s.letter_annotations['phred_quality'][-5:] = [2] * 5 processed = strip.processed_sequences(self.primer, [s], self.min_sequence_len, self.min_primer_match) self.assertEqual([], list(processed))