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src/b/i/biopython-1.63/Tests/test_pairwise2.py   biopython(Download)
    def test_match_score_open_penalty3(self):
        aligns = pairwise2.align.globalxs("GAACT", "GAT", -0.1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_extend_penalty1(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.5)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_extend_penalty2(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_penalize_extend_when_opening(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5, penalize_extend_when_opening=1)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_penalize_end_gaps(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.8, penalize_end_gaps=0)
        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_match_score_open_penalty3(self):
        aligns = pairwise2.align.globalxs("GAACT", "GAT", -0.1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_extend_penalty1(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.5)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_extend_penalty2(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_penalize_extend_when_opening(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5, penalize_extend_when_opening=1)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
    def test_penalize_end_gaps(self):
        aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.8, penalize_end_gaps=0)
        self.assertEqual(len(aligns), 3)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]