def mod_transl_except(feat, value):
ret = []
mods = value
if not isinstance(mods, list):
mods = [mods]
for value in mods:
if value[:1] != "(" or value[-1:] != ")":
raise ValueError("Invalidly formatted transl_except: %s" % value)
parts = location.location_split(value[1:-1])
if len(parts) != 2:
raise ValueError("Failed to split transl_except: %s" % value)
if parts[0][:4] != "pos:":
raise ValueError("Invalid transl_except position: %s" % parts[0])
if parts[1][:3] != "aa:":
raise ValueError("Unknown transl_except modification: %s" % parts[1])
loc = location.parse_str(parts[0][4:])
acid = parts[1][3:].upper()
if acid not in bioseq.data.AMINO_ACID_TLC:
raise ValueError("Unknown Amino Acid code: %s" % acid)
ret.append(gbobj.GBObj({
"location": loc,
"modification": bioseq.data.AMINO_ACID_TLC[acid]
}))
return ret
def kw_contig(stream, kw):
_no_subkeys(stream, "CONTIG", kw)
return location.parse_str(''.join(kw["value"].split()))