def test_write_obs_record(self):
"""writes observed records"""
f = StringIO()
exp = "a\nb\nc\n"
write_obs_record(f, 'a')
write_obs_record(f, 'b')
write_obs_record(f, 'c')
f.seek(0)
obs = f.read()
self.assertEqual(obs, exp)
def test_write_obs_record(self):
"""writes observed records"""
f = StringIO()
exp = "a\nb\nc\n"
write_obs_record(f, 'a')
write_obs_record(f, 'b')
write_obs_record(f, 'c')
f.seek(0)
obs = f.read()
self.assertEqual(obs,exp)
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
write_obs_record(obs_records, accession)
continue
except:
failure_count += 1
continue
# verify the sequence is DNA. NCBI silently corrupts records
# every once and a while leading to crap in the sequence.
# Thanks NCBI.
seq_chars = set(sequence)
if not seq_chars.issubset(alpha):
logline = log_f("Corrupt sequence, accession: %s" % (accession))
logger.write(logline)
if verbose:
stdout.write(logline)
failure_count += 1
