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))
