def test_write_sequence(self):
"""writes a sequence"""
f = StringIO()
exp = ">abc\nAATTGG\n>efg\nATGGG\n"
write_sequence(f, "abc", "AATTGG")
write_sequence(f, "efg", "ATGGG")
f.seek(0)
obs = f.read()
self.assertEqual(obs, exp)
def test_write_sequence(self):
"""writes a sequence"""
f = StringIO()
exp = ">abc\nAATTGG\n>efg\nATGGG\n"
write_sequence(f, "abc", "AATTGG")
write_sequence(f, "efg", "ATGGG")
f.seek(0)
obs = f.read()
self.assertEqual(obs,exp)
logline = log_f("Corrupt sequence, accession: %s" % (accession))
logger.write(logline)
if verbose:
stdout.write(logline)
failure_count += 1
continue
# gg_record contains gb summary data
try:
gg_record = get_genbank_summary(next_record)
except KeyError, e:
failure_count += 1
continue
seen.add(accession)
write_sequence(sequences, accession, sequence)
write_gg_record(gg_records, gg_record)
write_obs_record(obs_records, accession)
if failure_count >= max_failures:
logline = log_f("MAX FAILURES OF %d REACHED IN %s" % (max_failures, \
gb_fp))
logger.write(logline)
stderr.write(logline)
else:
logline = log_f("Parsed %s, %d failures observed." % (gb_fp, \
failure_count))
logger.write(logline)
if verbose:
stdout.write(logline)