test_alpha_rarefaction.py 文件源码

def test_alpha_rarefaction_with_phylogeny_and_metadata(self):
        t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
                       ['O1', 'O2'],
                       ['S1', 'S2', 'S3'])
        p = skbio.TreeNode.read(io.StringIO(
            '((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
        md = qiime2.Metadata(
            pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
                         index=['S1', 'S2', 'S3']))

        with tempfile.TemporaryDirectory() as output_dir:
            alpha_rarefaction(output_dir, t, max_depth=200, phylogeny=p,
                              metadata=md)
            index_fp = os.path.join(output_dir, 'index.html')
            self.assertTrue(os.path.exists(index_fp))
            self.assertTrue('observed_otus' in open(index_fp).read())
            self.assertTrue('shannon' in open(index_fp).read())
            self.assertTrue('faith_pd' in open(index_fp).read())