def test_search(self):
tax = taxonomy.Taxonomy()
res = tax.search("yeast", )
self.assertIn("4932", res)
res = tax.search("human", exact=True)
self.assertEqual(res, ["9606"])
def setUp(self):
self.common_ids = taxonomy.common_taxids()
self.organisms = [(taxonomy.name(tax_id), tax_id) for tax_id in self.common_ids]
self.taxon = taxonomy.Taxonomy()
def test_lineage(self):
tax = taxonomy.Taxonomy()
lineage = tax._tax.lineage("9606")
self.assertEqual(lineage[0], "1")
self.assertEqual(lineage[-1], "9605")
def test_other_names(self):
tax = taxonomy.Taxonomy()
names = tax.other_names("4932")
self.assertIn(("brewer's yeast", "common name"), names)
self.assertIn(("baker's yeast", 'genbank common name'), names)
def test_name(self):
tax = taxonomy.Taxonomy()
self.assertEqual(tax["9606"], "H**o sapiens")
self.assertEqual(tax["4932"], "Saccharomyces cerevisiae")
def test_other_names(self):
tax = taxonomy.Taxonomy()
names = tax.other_names("4932")
self.assertIn(("brewer's yeast", "common name"), names)
self.assertIn(("lager beer yeast", "common name"), names)