def test_species_below():
engine = create_engine('sqlite:///../testfiles/taxonomy.db', echo=False)
tax = Taxonomy(engine, taxtastic.ncbi.RANKS)
t = tax.species_below('1239')
parent_id, rank = tax._node(t)
for t in [None, '1239', '186801', '1117']:
s = tax.species_below(t)
assert t is None or s is None or tax.is_ancestor_of(s, t)
assert s is None or tax.rank(s) == 'species'
def test_lonely_company():
if not(os.path.exists('../testfiles/taxonomy.db')):
return
engine = create_engine('sqlite:///../testfiles/taxonomy.db', echo=False)
tax = Taxonomy(engine, ncbi.ranks)
print tax.lineage(49896)
lonely_tax_ids = [None, 816, 1239]
for a,t in zip(lonely_tax_ids, lonely_company(tax, lonely_tax_ids)):
assert a is None or t is None or tax.is_ancestor_of(t, tax.parent_id(a))
assert t is None or tax.rank(t) == 'species'
def test_is_ancestor_of():
engine = create_engine('sqlite:///../testfiles/taxonomy.db', echo=False)
tax = Taxonomy(engine, taxtastic.ncbi.RANKS)
assert tax.is_ancestor_of('1280', '1239')
assert tax.is_ancestor_of(None, '1239') is False
assert tax.is_ancestor_of('1239', None) is False