Python _compute_substitution_scoreの例

コード例 #1

    def test_compute_substitution_score(self):
        # these results were computed manually
        subs_m = make_identity_substitution_matrix(5, -4)
        gap_chars = set('-.')

        self.assertEqual(
            _compute_substitution_score(['A'], ['A'], subs_m, 0, gap_chars),
            5.0)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A'], subs_m, 0,
                                        gap_chars), 5.0)
        self.assertEqual(
            _compute_substitution_score(['A', 'C'], ['A'], subs_m, 0,
                                        gap_chars), 0.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'C'], ['A', 'C'], subs_m, 0,
                                        gap_chars), 0.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 0,
                                        gap_chars), 2.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 1,
                                        gap_chars), 3)

        # alt subs_m
        subs_m = make_identity_substitution_matrix(1, -2)

        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 0,
                                        gap_chars), 0.5)

コード例 #2

ファイル: test_pairwise.py プロジェクト: 7924102/scikit-bio

    def test_compute_substitution_score(self):
        # these results were computed manually
        subs_m = make_identity_substitution_matrix(5, -4)
        self.assertEqual(
            _compute_substitution_score(['A'], ['A'], subs_m, 0), 5.0)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A'], subs_m, 0), 5.0)
        self.assertEqual(
            _compute_substitution_score(['A', 'C'], ['A'], subs_m, 0), 0.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'C'], ['A', 'C'], subs_m, 0),
            0.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 0),
            2.5)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 1), 3)

        # alt subs_m
        subs_m = make_identity_substitution_matrix(1, -2)
        self.assertEqual(
            _compute_substitution_score(['A', 'A'], ['A', '-'], subs_m, 0),
            0.5)