def test_split_taxa(self):
known_taxa = np.array([['Bacteria', 'cont. Proteobacteria',
'Gammaproteobacteria',
'c. Gammaproteobacteria',
'c. Gammaproteobacteria',
'c. Gammaproteobacteria',
'c. Gammaproteobacteria'],
['Bacteria', 'Proteobacteria',
'Gammaproteobacteria', 'Enterobacteriales',
'Enterbacteriaceae', 'Escherichia', 'coli']],
dtype='|S32')
known_levels = ['kingdom', 'phylum', 'p_class', 'p_order', 'family',
'genus', 'species']
test_taxa, test_levels = split_taxa(self.taxa, 7)
self.assertEqual(known_levels, test_levels)
npt.assert_array_equal(known_taxa, test_taxa)
def test_split_taxa(self):
known_taxa = np.array([[
'Bacteria', 'cont. Proteobacteria', 'Gammaproteobacteria',
'c. Gammaproteobacteria', 'c. Gammaproteobacteria',
'c. Gammaproteobacteria', 'c. Gammaproteobacteria'
],
[
'Bacteria', 'Proteobacteria',
'Gammaproteobacteria', 'Enterobacteriales',
'Enterbacteriaceae', 'Escherichia', 'coli'
]],
dtype='|S32')
known_levels = [
'kingdom', 'phylum', 'p_class', 'p_order', 'family', 'genus',
'species'
]
test_taxa, test_levels = split_taxa(self.taxa, 7)
self.assertEqual(known_levels, test_levels)
npt.assert_array_equal(known_taxa, test_taxa)
def test_split_taxa_error(self):
with self.assertRaises(ValueError):
split_taxa(['k__Bacteria; p__[Proteobacteria]; '
'c__Gammaproteobacteria'], 7)
def test_split_taxa_error(self):
with self.assertRaises(ValueError):
split_taxa([
'k__Bacteria; p__[Proteobacteria]; '
'c__Gammaproteobacteria'
], 7)