def test_init(self):
"""NcbiNameLookup should map taxon ids to scientific names"""
names = list(NcbiNameParser(good_names)) # list of objects
sci_names = NcbiNameLookup(names) # NcbiNameLookup object
root = names[1] # NcbiName object made from 2nd line of good_name_file
bacteria = names[2] # from 3rd line of good_name_file
azorhizobium = names[7]
caulinodans = names[8]
assert sci_names[1] is root # gets NcbiName object from the
assert sci_names[2] is bacteria # NcbiNameLookup object and
assert sci_names[6] is azorhizobium # asks if it is the original
assert sci_names[7] is caulinodans # NcbiName object
self.assertEqual(sci_names[1].Name, "root")
self.assertEqual(sci_names[2].Name, "Bacteria")
self.assertEqual(sci_names[7].Name, "Azorhizobium caulinodans")
self.assertEqual(sci_names[9].Name, "Buchnera aphidicola")
def setUp(self):
"""Sets up the class tests"""
self.names = list(NcbiNameParser(good_names))
self.nodes = list(NcbiTaxonParser(good_nodes))
self.taxID_to_obj = NcbiTaxonLookup(self.nodes)
self.names_to_obj = NcbiNameLookup(self.names)