def test_motif_pyrimidine_run(self):
seq = DNA("")
self.assertEqual(list(seq.find_motifs("pyrimidine-run")), [])
seq = DNA("AARC--TCRA")
self.assertEqual(list(seq.find_motifs("pyrimidine-run")),
[slice(3, 4), slice(6, 8)])
seq = DNA("AA-RC--TCR-A")
self.assertEqual(list(seq.find_motifs("pyrimidine-run", min_length=3,
ignore=seq.gaps())),
[slice(4, 9)])
def test_motif_purine_run(self):
seq = DNA("")
self.assertEqual(list(seq.find_motifs("purine-run")), [])
seq = DNA("AARC--TCRG")
self.assertEqual(list(seq.find_motifs("purine-run")),
[slice(0, 3), slice(8, 10)])
seq = DNA("AA-RC--TCR-G")
self.assertEqual(
list(seq.find_motifs("purine-run", min_length=3,
ignore=seq.gaps())), [slice(0, 4)])
def test_motif_purine_run(self):
seq = DNA("")
self.assertEqual(list(seq.find_motifs("purine-run")), [])
seq = DNA("AARC--TCRG")
self.assertEqual(list(seq.find_motifs("purine-run")),
[slice(0, 3), slice(8, 10)])
seq = DNA("AA-RC--TCR-G")
self.assertEqual(list(seq.find_motifs("purine-run", min_length=3,
ignore=seq.gaps())),
[slice(0, 4)])
def test_motif_pyrimidine_run(self):
seq = DNA("")
self.assertEqual(list(seq.find_motifs("pyrimidine-run")), [])
seq = DNA("AARC--TCRA")
self.assertEqual(list(seq.find_motifs("pyrimidine-run")),
[slice(3, 4), slice(6, 8)])
seq = DNA("AA-RC--TCR-A")
self.assertEqual(
list(
seq.find_motifs("pyrimidine-run",
min_length=3,
ignore=seq.gaps())), [slice(4, 9)])