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