def test_get_accession(self): """Get an accession""" exp_gb1 = "AGIY01000001.1" exp_gb2 = "FO117587.1" obs_gb1 = get_accession(self.gb1) obs_gb2 = get_accession(self.gb2) self.assertEqual(obs_gb1, exp_gb1) self.assertEqual(obs_gb2, exp_gb2)
next_record = records.next() except PartialRecordError, e: failure_count += 1 continue except StopIteration: break except Exception, e: logline = log_f("Caught: %s, previous accession: %s" % (e, accession)) logger.write(logline) if verbose: stdout.write(logline) failure_count += 1 # accession is str including version try: accession = get_accession(next_record) except: failure_count += 1 continue if accession in observed_records: continue if accession in seen: continue # accession added at the end of this while loop # sequence is just a str of sequence try: sequence = get_sequence(next_record) except NoSequenceError: # this isn't a failure, so no point in continuing but record # the accession so it isn't hit again