def test_get_reference_taxonomy(self): fp = get_reference_taxonomy() self.assertIn( os.path.join('gg_13_8_otus', 'taxonomy', '97_otu_taxonomy.txt'), fp) self.assertTrue(os.path.isfile(fp)) self.assertTrue(os.path.isabs(fp)) with open(fp, 'rb') as f: md5 = safe_md5(f).hexdigest() self.assertEqual(md5, '56ef15dccf2e931ec173f4f977ed649b')
def get_reference_set(): """Get the reference set to use for OTU picking Returns ------- str The file path to the reference sequences. str The file path to the reference taxonomy. """ if ag.is_test_env(): repo = get_repository_dir() ref_seqs = os.path.join(repo, 'tests/data/otus.fna') ref_tax = os.path.join(repo, 'tests/data/otus.txt') return ref_seqs, ref_tax else: return qdr.get_reference_sequences(), qdr.get_reference_taxonomy()
def defineTaxSeqsFile(uploadedSeqsFile): # uploadSeqsFile(uploadedSeqsFile) return compareWithDB(uploadedSeqsFile, qdr.get_reference_sequences(), qdr.get_reference_taxonomy())