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src/b/i/bioa-1.24/bioa/io/amplicon.py   bioa(Download)
    def _best(reference, seq):
        return max(align.localds(reference, seq, match_matrix,
                    open_gap, extend_gap))
 
    se_positions = []

src/b/i/biopython-1.63/Tests/test_pairwise2.py   biopython(Download)
    def test_match_dictionary1(self):
        aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -.5, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_dictionary2(self):
        aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -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_match_dictionary3(self):
        aligns = pairwise2.align.localds("ATT", "ATAT", self.match_dict, -1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)

src/b/i/biopython-HEAD/Tests/test_pairwise2.py   biopython(Download)
    def test_match_dictionary1(self):
        aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -.5, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_dictionary2(self):
        aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -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_match_dictionary3(self):
        aligns = pairwise2.align.localds("ATT", "ATAT", self.match_dict, -1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)