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