def test_subst_ranks(self): testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles") tax_fname = os.path.join(testfile_dir, "test.tax") tax = Taxonomy("", tax_fname) old_ranks = tax.get_seq_ranks("WgeSangu") self.assertEqual(old_ranks[-2], 'Sneathia') syn_map = {'Sneathia' : 'Sebaldella'} tax.subst_synonyms(syn_map) new_ranks = tax.get_seq_ranks("WgeSangu") self.assertEqual(old_ranks[-2], 'Sebaldella')
def test_normalize_rank_names(self): tax = Taxonomy(tax_map=self.taxonomy.seq_ranks_map) ranks = tax.get_seq_ranks("UpbRectu") self.assertEqual(ranks[0], "[Bacteria]") self.assertEqual(ranks[1], "'Firmicutes'") self.assertEqual(ranks[2], "Clostridia(1)") corr_ranks = tax.normalize_rank_names() self.assertEqual(len(corr_ranks), 3) ranks = tax.get_seq_ranks("UpbRectu") self.assertEqual(ranks[0], "_Bacteria_") self.assertEqual(ranks[1], "_Firmicutes_") self.assertEqual(ranks[2], "Clostridia_1_")