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src/b/i/biopython-1.63/Tests/test_pairwise2.py   biopython(Download)
    def test_separate_gap_penalties1(self):
        aligns = pairwise2.align.localxd("GAT", "GTCT", -0.3, 0, -0.8, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_separate_gap_penalties2(self):
        aligns = pairwise2.align.localxd("GAT", "GTCT", -0.5, 0, -0.2, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_separate_gap_penalties_with_extension(self):
        aligns = pairwise2.align.localxd(list("GAAT"), list("GTCCT"), -0.1, 0, -0.1, -0.1, gap_char=["-"])
        self.assertEqual(len(aligns), 3)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]

src/b/i/biopython-HEAD/Tests/test_pairwise2.py   biopython(Download)
    def test_separate_gap_penalties1(self):
        aligns = pairwise2.align.localxd("GAT", "GTCT", -0.3, 0, -0.8, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_separate_gap_penalties2(self):
        aligns = pairwise2.align.localxd("GAT", "GTCT", -0.5, 0, -0.2, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_separate_gap_penalties_with_extension(self):
        aligns = pairwise2.align.localxd(list("GAAT"), list("GTCCT"), -0.1, 0, -0.1, -0.1, gap_char=["-"])
        self.assertEqual(len(aligns), 3)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]