def test_validate_taxrank_taxmap_taxtree_fail2(self):
# test for case which taxmap file has more taxids
# than is present in the taxonomy tree.
input_taxrank = _prep_taxranks(self.taxranks)
input_taxmap = _prep_taxmap(self.taxmap)
self.assertRaises(ValueError, _validate_taxrank_taxmap_taxtree,
input_taxrank, input_taxmap, self.taxtree)
def test_prep_taxmap(self):
obs_taxmap = _prep_taxmap(self.taxmap)
obs_taxmap.sort_index(inplace=True)
dm = {
'Feature ID': [
'A16379.1.1485', 'A45315.1.1521', 'A61579.1.1437',
'AAAA02020713.1.1297', 'AAAA02020714.1.1202',
'AAAA02038450.2584.4394', 'AAAA02039541.11.1886',
'AAAA02041579.2617.4209', 'AAAA02046270.117.1956',
'AAAA02048270.689.2185'
],
'organism_name': [
'[Haemophilus]_ducreyi', 'Bacillus_sp.',
'Thermopallium_natronophilum', 'Oryza_sativa', 'Oryza_sativa',
'Oryza_sativa', 'Oryza_sativa', 'Oryza_sativa', 'Oryza_sativa',
'Oryza_sativa'
],
'taxid': [
'3698', '45177', '46692', '46463', '2852', '10099', '47183',
'4432', '4432', '44317'
]
}
exp_taxmap = pd.DataFrame(dm)
exp_taxmap.set_index('Feature ID', inplace=True)
exp_taxmap.sort_index(inplace=True)
assert_frame_equal(obs_taxmap, exp_taxmap)
def test_validate_taxrank_taxmap_taxtree_pass(self):
# all files should meet the criteria and return None
input_taxrank = _prep_taxranks(self.taxranks)
input_taxmap = _prep_taxmap(self.taxmap2)
exp = _validate_taxrank_taxmap_taxtree(input_taxrank, input_taxmap,
self.taxtree)
self.assertEqual(None, exp)
def test_compile_taxonomy_output_default(self):
input_taxrank = _prep_taxranks(self.taxranks)
silva_tax = _build_base_silva_taxonomy(self.taxtree, input_taxrank,
ALLOWED_RANKS,
rank_propagation=True)
input_taxmap = _prep_taxmap(self.taxmap2)
updated_taxmap = pd.merge(input_taxmap, silva_tax, left_on='taxid',
right_index=True)
obs_6r_tax = _compile_taxonomy_output(updated_taxmap,
ranks=DEFAULT_RANKS,
include_species_labels=False)
obs_6r_tax.sort_index(inplace=True)
# expected 6-rank taxonomy
t1 = ("d__Archaea; p__Aenigmarchaeota; c__Aenigmarchaeia; "
"o__Aenigmarchaeales; f__Aenigmarchaeales; "
"g__Candidatus_Aenigmarchaeum")
exp_6r_tax = pd.Series(t1, index=['AB600437.1.1389'])
exp_6r_tax.rename('Taxon', inplace=True)
exp_6r_tax.index.name = 'Feature ID'
exp_6r_tax.sort_index(inplace=True)
assert_series_equal(obs_6r_tax, exp_6r_tax)
def test_validate_taxrank_taxmap_taxtree_fail(self):
# test for missing taxid in tree file
input_taxrank = _prep_taxranks(self.taxranks)
input_taxmap = _prep_taxmap(self.taxmap2)
self.assertRaises(ValueError, _validate_taxrank_taxmap_taxtree,
input_taxrank, input_taxmap, self.taxtree2)