def test_qza_integration(self):
table_qza = Artifact.import_data("FeatureTable[Frequency]", self.table)
taxonomy_qza = Artifact.import_data(
"FeatureData[Taxonomy]",
self.taxonomy_df,
)
table = table_qza.view(biom.Table)
taxonomy_df = taxonomy_qza.view(pd.DataFrame)
taxonomy = Taxonomy(table, taxonomy_df)
taxonomy.get_group(['sample-1', 'sample-2'], 'foo')
def test_get_group(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df)
exp = GroupTaxonomy(name='sample-2',
taxonomy='((((feature-1,((feature-2)e)d)c)b)a);',
features=['feature-1', 'feature-2'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
obs = taxonomy.get_group(['sample-2'])
self.assertEqual(obs, exp)
def test_get_group_with_variances(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df, self.table_vars)
exp = GroupTaxonomy(
name='sample-1',
taxonomy='((((((feature-2)e)d)c)b,(((feature-3)h)g)f)a);', # noqa
features=['feature-2', 'feature-3'],
feature_values=[2. / 5, 3. / 5],
feature_variances=[2.0, 3.0])
obs = taxonomy.get_group(['sample-1'])
self.assertEqual(obs, exp)
def test_get_group_multiple(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df)
exp = GroupTaxonomy(
name='foo',
taxonomy=
'((((feature-1,((feature-2)e)d)c)b,(((feature-3)h)g)f)a);', # noqa
features=['feature-1', 'feature-2', 'feature-3'],
feature_values=[1. / 10, 6. / 10, 3. / 10],
feature_variances=[0.0, 0.0, 0.0])
obs = taxonomy.get_group(['sample-1', 'sample-2'], 'foo')
self.assertEqual(obs.name, exp.name)
self.assertEqual(obs.taxonomy, exp.taxonomy)
self.assertEqual(obs.features, exp.features)
npt.assert_almost_equal(obs.feature_values, exp.feature_values)
self.assertEqual(obs.feature_variances, exp.feature_variances)
def test_get_group_missing(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df)
with self.assertRaisesRegex(UnknownID, "sample-X does not exist"):
taxonomy.get_group(['sample-X'])