def embl_gb_fasta(raw, ds, path=None):
pattern = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
result_list = []
rawseqs = _re.findall(pattern, _textwrap.dedent(raw + "\n\n"), flags=_re.MULTILINE)
for rawseq in rawseqs:
format_ = None
handle = _io.StringIO(rawseq)
if "circular" in rawseq.splitlines()[0]:
circular = True
else:
circular = False
try:
parsed = _SeqIO.read(handle, "embl", alphabet=_IUPACAmbiguousDNA())
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "genbank", alphabet=_IUPACAmbiguousDNA())
handle.seek(0)
parser = _RecordParser()
residue_type = parser.parse(handle).residue_type
if "circular" in residue_type :
circular = True
else:
try:
if parsed.annotations["topology"] == "circular":
circular = True
else:
circular = False
except KeyError:
circular = False
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "fasta", alphabet=_IUPACAmbiguousDNA())
except ValueError:
parsed = ""
else: format_= "fasta"
else: format_= "genbank"
else: format_ = "embl"
handle.close()
if parsed:
from copy import deepcopy as _deepcopy ## TODO: clean up !
from pydna.seqfeature import SeqFeature as _SeqFeature
nfs = [_SeqFeature() for f in parsed.features]
for f, nf in zip(parsed.features, nfs):
nf.__dict__ =_deepcopy(f.__dict__)
parsed.features = nfs
if ds and path:
result_list.append( _GenbankFile.from_SeqRecord(parsed, linear=not circular, circular=circular, path=path) )
elif ds:
result_list.append ( _Dseqrecord.from_SeqRecord(parsed, linear=not circular, circular=circular) )
else:
result_list.append( parsed )
return result_list
def embl_gb_fasta(raw, ds, path=None):
pattern = (r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|"
r"LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)")
result_list = []
rawseqs = _re.findall(pattern,
_textwrap.dedent(raw + "\n\n"),
flags=_re.MULTILINE)
for rawseq in rawseqs:
handle = _io.StringIO(rawseq)
circular = False
try:
parsed = _SeqIO.read(handle, "embl")
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "genbank")
if "circular" in str(
parsed.annotations.get("topology")).lower():
circular = True
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "fasta")
except ValueError:
parsed = ""
handle.close()
if ("circular" in rawseq.splitlines()[0].lower().split()
): # hack to pick up topology from malformed files
circular = True
if parsed:
from copy import deepcopy as _deepcopy # TODO: clean up !
from pydna.seqfeature import SeqFeature as _SeqFeature
nfs = [_SeqFeature() for f in parsed.features]
for f, nf in zip(parsed.features, nfs):
nf.__dict__ = _deepcopy(f.__dict__)
parsed.features = nfs
if ds and path:
result_list.append(
_GenbankFile.from_SeqRecord(parsed,
linear=not circular,
circular=circular,
path=path))
elif ds:
result_list.append(
_Dseqrecord.from_SeqRecord(parsed,
linear=not circular,
circular=circular))
else:
result_list.append(parsed)
return result_list
