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