def test_primer_provided(self):
res = quality_filter.parse_barcode_file(self.fp, primer='CATTGCCTATG')
self.assertEqual(9, len(res.keys()))
self.assertEqual('p1d1bc210', res['TACAGTCGCATTGCCTATG'])
self.assertEqual(None, triefind.match('TACAGTCGCATTGCCTAT', res))
self.assertEqual('TACAGTCGCATTGCCTATG',
triefind.match('TACAGTCGCATTGCCTATGCTACCTA', res))
def test_primer_provided(self):
res = quality_filter.parse_barcode_file(self.fp, primer='CATTGCCTATG')
self.assertEqual(9, len(list(res.keys())))
self.assertEqual('p1d1bc210', res['TACAGTCGCATTGCCTATG'])
self.assertEqual(None, triefind.match('TACAGTCGCATTGCCTAT', res))
self.assertEqual('TACAGTCGCATTGCCTATG',
triefind.match('TACAGTCGCATTGCCTATGCTACCTA', res))
def test_primer_in_file(self):
res = quality_filter.parse_barcode_file(self.fp, primer=None)
self.assertEqual(13, len(res.keys()))
# Test ambiguities
self.assertEqual('p1d1bc212', res['TACGTCTCCATGGCTA'])
self.assertEqual('p1d1bc212', res['TACGTCTCCACGGCTA'])
self.assertIsNone(res.get('TACGTCTCCAAGGCTA'))
self.assertIsNone(res.get('TACGTCTCCAGGGCTA'))
def test_primer_in_file(self):
res = quality_filter.parse_barcode_file(self.fp, primer=None)
self.assertEqual(13, len(res.keys()))
# Test ambiguities
self.assertEqual('p1d1bc212', res['TACGTCTCCATGGCTA'])
self.assertEqual('p1d1bc212', res['TACGTCTCCACGGCTA'])
self.assertIsNone(res.get('TACGTCTCCAAGGCTA'))
self.assertIsNone(res.get('TACGTCTCCAGGGCTA'))
def setUp(self):
self.sequences = [SeqRecord(Seq('ACCGTTACGAT'), 'seq1'),
SeqRecord(Seq('ACTGTTACGCT'), 'seq2'),
SeqRecord(Seq('AACTGTTA'), 'seq3'), # Homopolymer in bc
SeqRecord(Seq('ACCGTA'), 'seq4'), # Error in primer
]
barcode_str = """Sample1,ACC\nSample2,ACT\n"""
self.primer = 'GTTA'
self.trie = quality_filter.parse_barcode_file(StringIO(barcode_str), primer=self.primer)
self.outfile = StringIO()
self.instance = quality_filter.PrimerBarcodeFilter(self.trie, self.outfile)
def setUp(self):
self.sequences = [
SeqRecord(Seq('ACCGTTACGAT'), 'seq1'),
SeqRecord(Seq('ACTGTTACGCT'), 'seq2'),
SeqRecord(Seq('AACTGTTA'), 'seq3'), # Homopolymer in bc
SeqRecord(Seq('ACCGTA'), 'seq4'), # Error in primer
]
barcode_str = """Sample1,ACC\nSample2,ACT\n"""
self.primer = 'GTTA'
self.trie = quality_filter.parse_barcode_file(StringIO(barcode_str),
primer=self.primer)
self.outfile = StringIO()
self.instance = quality_filter.PrimerBarcodeFilter(
self.trie, self.outfile)
