def test_relabel_stratified_taxonomy_unknown_species(self):
species = ('k__Bacteria; p__Firmicutes; c__Bacilli; '
'o__Lactobacillales; f__Lactobacillaceae; '
'g__Lactobacillus; s__reuteri')
exp = ('k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; '
'f__Lactobacillaceae; g__Lactobacillus')
obs = cross_validate._relabel_stratified_taxonomy(
species, self.valid_taxonomies)
self.assertEqual(exp, obs)
def test_relabel_stratified_taxonomy_unknown_kingdom(self):
species = 'k__Peanut'
with self.assertRaisesRegex(RuntimeError, "unknown kingdom"):
cross_validate._relabel_stratified_taxonomy(
species, self.valid_taxonomies)