test_beta.py 文件源码

def test_beta_phylogenetic(self):
        t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
                  ['O1', 'O2'],
                  ['S1', 'S2', 'S3'])
        tree = skbio.TreeNode.read(io.StringIO(
            '((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
        actual = beta_phylogenetic(
            table=t, phylogeny=tree, metric='unweighted_unifrac')
        # expected computed with skbio.diversity.beta_diversity
        expected = skbio.DistanceMatrix([[0.00, 0.25, 0.25],
                                         [0.25, 0.00, 0.00],
                                         [0.25, 0.00, 0.00]],
                                        ids=['S1', 'S2', 'S3'])

        self.assertEqual(actual.ids, expected.ids)
        for id1 in actual.ids:
            for id2 in actual.ids:
                npt.assert_almost_equal(actual[id1, id2], expected[id1, id2])