Beispiel #1
0
    def test_distance_matrix_smooth(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, do_smooth=True, precision=3)

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.077', '0.000 0.077']
Beispiel #2
0
    def test_distance_matrix_smooth(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, do_smooth=True, precision=3)

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.077', '0.000 0.077']
Beispiel #3
0
    def test_distance_matrix_pairwise_name(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, precision=3,
                                         custom_pairwise='numpy.multiply')

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.084', '1.206 0.084']
Beispiel #4
0
    def test_distance_matrix_pairwise_expr(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, precision=3,
                                         custom_pairwise='abs(left - right) / (left + right + 1000)')

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.001', '0.000 0.001']
Beispiel #5
0
    def test_distance_matrix_pairwise_name(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, precision=3,
                                         custom_pairwise='numpy.multiply')

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.084', '1.206 0.084']
Beispiel #6
0
    def test_distance_matrix_pairwise_expr(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.multi_profile(8,
                                                   [counts_left,
                                                    counts_right,
                                                    counts_left],
                                                   ['a', 'b', 'c'])) as handle:
                    kmer.distance_matrix(handle, out, precision=3,
                                         custom_pairwise='abs(left - right) / (left + right + 1000)')

        assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.001', '0.000 0.001']