def test_alpha_phylogenetic_alt_unknown_metric(self):
table = self.get_data_path('two_feature_table.biom')
tree = self.get_data_path('three_feature.tree')
with self.assertRaisesRegex(ValueError, 'Unknown phylogenetic metric'):
alpha_phylogenetic_alt(table=table,
phylogeny=tree,
metric='not-a-metric')
def test_alpha_phylogenetic_alt_empty_table(self):
table = self.get_data_path('empty.biom')
tree = self.get_data_path('three_feature.tree')
with self.assertRaisesRegex(ValueError, "empty"):
alpha_phylogenetic_alt(table=table,
phylogeny=tree,
metric='faith_pd')
def test_alpha_phylogenetic_alt_skbio_error_rewriting(self):
table = self.get_data_path('two_feature_table.biom')
tree = self.get_data_path('vaw.nwk')
with self.assertRaisesRegex(ValueError, "The table does not "
"appear to be completely represented "
"by the phylogeny."):
alpha_phylogenetic_alt(table=table,
phylogeny=tree,
metric='faith_pd')
def test_alpha_phylogenetic_alt(self):
table = self.get_data_path('two_feature_table.biom')
tree = self.get_data_path('three_feature.tree')
actual = alpha_phylogenetic_alt(table=table,
phylogeny=tree,
metric='faith_pd')
# expected computed with skbio.diversity.alpha_diversity
expected = pd.Series({'S1': 0.75, 'S2': 1.0, 'S3': 1.0},
name='faith_pd')
pdt.assert_series_equal(actual, expected)