示例#1
0
    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)])
示例#2
0
    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)])
示例#3
0
    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)])
示例#4
0
    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)])