test_alpha_rarefaction.py 文件源码

def test_alpha_rarefaction_with_empty_column_in_metadata(self):
        t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
                       ['O1', 'O2'],
                       ['S1', 'S2', 'S3'])
        md = qiime2.Metadata(
            pd.DataFrame({'pet': ['russ', 'milo', 'peanut', 'summer'],
                          'foo': [np.nan, np.nan, np.nan, 'bar']},
                         index=['S1', 'S2', 'S3', 'S4']))
        with tempfile.TemporaryDirectory() as output_dir:
            alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)

            index_fp = os.path.join(output_dir, 'index.html')
            self.assertTrue(os.path.exists(index_fp))
            with open(index_fp, 'r') as fh:
                contents = fh.read()

            self.assertTrue('observed_otus' in contents)
            self.assertTrue('shannon' in contents)
            self.assertTrue('did not contain any values:' in contents)

            metric_fp = os.path.join(output_dir, 'shannon-pet.jsonp')
            self.assertTrue('summer' not in open(metric_fp).read())
            self.assertFalse(
                os.path.exists(os.path.join(output_dir, 'shannon-foo.jsonp')))