def test_seed_extend_medium_gap(self):
target = seq3 + seq2 + QUERY + seq2[:24] + QUERY + seq2 + seq3
matching_intervals = py_seed_extend(QUERY + QUERY, target)
self.assertEqual(matching_intervals.shape[0], 1)
self.assertLessEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 110)
self.assertGreaterEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 90)
def test_seed_extend_small_gap(self):
target = seq3 + seq2 + QUERY + seq2 + seq3
gap = 'AAAAA'
matching_intervals = py_seed_extend(QUERY[:24] + gap + QUERY[24:],
target)
self.assertEqual(matching_intervals.shape[0], 1)
self.assertLessEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 60)
self.assertGreaterEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 40)
def test_seed_extend_continues(self):
target = seq3 + seq2 + QUERY + QUERY + seq2 + seq3
matching_intervals = py_seed_extend(QUERY + QUERY, target)
self.assertEqual(matching_intervals.shape[0], 1)
self.assertEqual(matching_intervals[0, 1] - matching_intervals[0, 0],
matching_intervals[0, 3] - matching_intervals[0, 2])
self.assertLessEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 110)
self.assertGreaterEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 90)
def test_seed_extend_big_gap(self):
target = seq3 + seq2 + QUERY + seq2 + seq3 + seq2 + seq3 + seq2 + QUERY + seq2 + seq3
matching_intervals = py_seed_extend(QUERY + QUERY, target)
self.assertEqual(matching_intervals.shape[0], 2)
self.assertLessEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 60)
self.assertGreaterEqual(
matching_intervals[0, 1] - matching_intervals[0, 0], 40)
self.assertLessEqual(
matching_intervals[1, 1] - matching_intervals[1, 0], 60)
self.assertGreaterEqual(
matching_intervals[1, 1] - matching_intervals[1, 0], 40)