Example #1
0
    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"])
Example #2
0
 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()
Example #3
0
 def test_lineage(self):
     tax = taxonomy.Taxonomy()
     lineage = tax._tax.lineage("9606")
     self.assertEqual(lineage[0], "1")
     self.assertEqual(lineage[-1], "9605")
Example #4
0
    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)
Example #5
0
 def test_name(self):
     tax = taxonomy.Taxonomy()
     self.assertEqual(tax["9606"], "H**o sapiens")
     self.assertEqual(tax["4932"], "Saccharomyces cerevisiae")
Example #6
0
    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)