def test_N_boundary_positions(self):
boundaries = find_N_boundaries(self.src_seq)
self.assertTupleEqual(boundaries, (16, 33))
self.assertEqual(self.src_seq[16], 'T')
self.assertEqual(self.src_seq[33], 'C')
boundaries = find_N_boundaries(self.fwd_seq)
self.assertTupleEqual(boundaries, (0, 33))
boundaries = find_N_boundaries(self.rev_seq)
self.assertTupleEqual(boundaries, (16, 46))
self.assertEqual(self.rev_seq[46], 'T')
self.assertEqual(self.rev_seq[33], 'C')
def test_elongate_reverse_sequence_kmer_mode(self):
boundaries = find_N_boundaries(self.src_seq)
hexamer_table = build_hexamer_table()
hexamer_pair = determine_hexamers(self.src_seq, boundaries,
hexamer_table)
tst_seq = elongate_reverse_sequence(self.src_seq, hexamer_pair[1],
"kmer_mode")
self.assertEqual(len(tst_seq), len(self.rev_seq))
self.assertEqual(tst_seq, self.rev_seq)
def test_elongate_forward_sequence(self):
boundaries = find_N_boundaries(self.src_seq)
hexamer_table = build_hexamer_table()
hexamer_pair = determine_hexamers(self.src_seq, boundaries,
hexamer_table)
tst_seq = elongate_forward_sequence(self.src_seq, hexamer_pair[0],
"naive_mode")
self.assertEqual(len(tst_seq), len(self.fwd_seq))
self.assertEqual(tst_seq, self.fwd_seq)
def test_determine_hexamer(self):
boundaries = find_N_boundaries(self.src_seq)
hexamer_table = build_hexamer_table()
# Will find known pattern CCCTAA in sequence
hexamer_pair = determine_hexamers(self.src_seq, boundaries,
hexamer_table)
self.assertEqual('TAACCC', hexamer_pair[0])
self.assertEqual('TAACCC', hexamer_pair[1])
# Should not find any pattern in sequence
hexamer_pair = determine_hexamers(self.no_patt, boundaries,
hexamer_table)
self.assertNotIn('TAACCC', hexamer_pair)
self.assertEqual(hexamer_pair, [None, None])