def test_multiple_metrics(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_features', 'shannon']) exp_ind = pd.MultiIndex.from_product( [[1, 200], [1]], names=['_alpha_rarefaction_depth_column_', 'iter']) exp = pd.DataFrame(data=[[1, 2], [1, 2], [1, 2]], columns=exp_ind, index=['S1', 'S2', 'S3']) pdt.assert_frame_equal(obs['observed_features'], exp) exp = pd.DataFrame(data=[[0., 0.811278124459], [0., 1.], [0., 1.]], columns=exp_ind, index=['S1', 'S2', 'S3']) pdt.assert_frame_equal(obs['shannon'], exp)
def test_faith_pd(self): t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) p = skbio.TreeNode.read( io.StringIO('((O1:0.25, O2:0.50):0.25, O3:0.75)root;')) obs = _compute_rarefaction_data(feature_table=t, min_depth=1, max_depth=200, steps=2, iterations=1, phylogeny=p, metrics=['faith_pd']) self.assertTrue('faith_pd' in obs)
def test_faith_pd(self): t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) p = skbio.TreeNode.read(io.StringIO( '((O1:0.25, O2:0.50):0.25, O3:0.75)root;')) obs = _compute_rarefaction_data(feature_table=t, min_depth=1, max_depth=200, steps=2, iterations=1, phylogeny=p, metrics=['faith_pd']) self.assertTrue('faith_pd' in obs)
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)
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)