test_cluster_features.py 文件源码

def test_99_percent_clustering(self):
        exp_table = biom.Table(np.array([[104, 106, 109],
                                         [1, 1, 2],
                                         [7, 8, 9]]),
                               ['feature1', 'feature2',
                                'feature4'],
                               ['sample1', 'sample2', 'sample3'])

        with redirected_stdio(stderr=os.devnull):
            obs_table, obs_sequences = cluster_features_de_novo(
                sequences=self.input_sequences, table=self.input_table,
                perc_identity=0.99)
        # order of identifiers is important for biom.Table equality
        obs_table = \
            obs_table.sort_order(exp_table.ids(axis='observation'),
                                 axis='observation')
        self.assertEqual(obs_table, exp_table)

        # sequences are reverse-sorted by abundance in output
        obs_seqs = _read_seqs(obs_sequences)
        exp_seqs = [self.input_sequences_list[0], self.input_sequences_list[3],
                    self.input_sequences_list[1]]
        self.assertEqual(obs_seqs, exp_seqs)