def detect_format(config):
if 'format' not in config:
try:
filename = path(config['filename'])
with filename.open('r') as f:
header = f.read(5)
if filename.ext in ('.gb', '.gbk') or header.startswith('LOCUS'):
log.debug("Attempting %s as genbank", filename)
seqrec = genbank.parse_seq_rec(config['filename'])
config['format'] = 'genbank'
config['id'] = seqrec.id
config['description'] = seqrec.description
seq = str(seqrec.seq)
elif filename.ext in ('.fna', '.fasta') or header.startswith('>'):
seqrec = SeqIO.read(filename, 'fasta')
config['format'] = 'fasta'
config['id'] = seqrec.id
config['description'] = seqrec.description
seq = str(seqrec.seq)
else:
with filename.open('r') as f:
seq = f.read()
seq = re.sub('\s', '', seq)
config['format'] = 'raw'
config['length'] = len(seq)
ddna = derive_filename(config, filename.getmtime(), 'ddna')
if not ddna.exists():
with mkstemp_rename(ddna) as f:
f.write(seq.upper())
config['ddna'] = ddna
except:
log.exception("Error detecting format")
config['format'] = None
def test_mkstemp_rename(tmpdir):
filename = tmpdir.join('file')
with util.mkstemp_rename(str(filename)) as out:
out.write('foo')
assert len(tmpdir.listdir()) == 1
assert not filename.exists()
assert filename.exists()