test_alpha_rarefaction.py 文件源码

def test_observed_otus(self):
        t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
                       ['O1', 'O2'],
                       ['S1', 'S2', 'S3'])
        obs = _compute_rarefaction_data(feature_table=t,
                                        min_depth=1,
                                        max_depth=200,
                                        steps=2,
                                        iterations=1,
                                        phylogeny=None,
                                        metrics=['observed_otus'])

        exp_ind = pd.MultiIndex.from_product(
            [[1, 200], [1]],
            names=['depth', 'iter'])
        exp = pd.DataFrame(data=[[1, 2], [1, 2], [1, 2]],
                           columns=exp_ind,
                           index=['S1', 'S2', 'S3'])
        pdt.assert_frame_equal(obs['observed_otus'], exp)