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)
