def test_first_distances_baseline_invalid_baseline(self): with self.assertRaisesRegex(ValueError, "must be a valid state"): first_distances( distance_matrix=dm, metadata=qiime2.Metadata(md_one_subject_many_times), state_column='Time', individual_id_column='ind', replicate_handling='drop', baseline=27)
def test_first_distances_single_sample(self): with self.assertRaisesRegex(RuntimeError, "Output is empty"): first_distances(distance_matrix=dm_single_sample, metadata=qiime2.Metadata(md), state_column='Time', individual_id_column='ind', replicate_handling='drop')
def test_first_distances_ecam(self): exp = pd.read_csv(self.get_data_path( 'ecam-first-distances.tsv'), sep='\t', squeeze=True, index_col=0) obs = first_distances( distance_matrix=self.md_ecam_dm, metadata=self.md_ecam_fp, state_column='month', individual_id_column='studyid', replicate_handling='drop') pdt.assert_series_equal(obs, exp)
def test_first_distances(self): exp = pd.Series([0.1, 0.1, 0.3, 0.1, 0.2, 0.4], index=['3', '4', '5', '9', '10', '11'], name='Distance') exp.index.name = '#SampleID' obs = first_distances( distance_matrix=dm, metadata=qiime2.Metadata(md), state_column='Time', individual_id_column='ind', replicate_handling='drop') pdt.assert_series_equal(obs, exp)
def test_first_distances_one_subject_many_times(self): exp = pd.Series( [0.3, 0.9, 0.3, 0.2, 0.4, 0.4, 0.5, 0.8, 0.3, 0.4, 0.6], index=['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], name='Distance') exp.index.name = '#SampleID' obs = first_distances( distance_matrix=dm, metadata=qiime2.Metadata(md_one_subject_many_times), state_column='Time', individual_id_column='ind', replicate_handling='drop') pdt.assert_series_equal(obs, exp)