[Biopython-dev] Bio.GenBank.LocationParser chokes on misc_feature in Desulfurococcus kamchatkensis 1221n/NC_011766.gbk

[Tim te Beek]

When parsing ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Desulfurococcus_kamchatkensis_1221n_uid59133/NC_011766.gbk
using SeqIO.read(genbank_file, 'genbank') I get the following
stacktrace:

...
    gbk_records = (SeqIO.read(genbank_file, 'genbank') for
genbank_file in genbank_files)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/__init__.py",
line 604, in read
    first = iterator.next()
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/__init__.py",
line 532, in parse
    for r in i:
  File "/usr/local/lib/python2.6/dist-packages/Bio/GenBank/Scanner.py",
line 440, in parse_records
    record = self.parse(handle, do_features)
  File "/usr/local/lib/python2.6/dist-packages/Bio/GenBank/Scanner.py",
line 423, in parse
    if self.feed(handle, consumer, do_features):
  File "/usr/local/lib/python2.6/dist-packages/Bio/GenBank/Scanner.py",
line 395, in feed
    self._feed_feature_table(consumer, self.parse_features(skip=False))
  File "/usr/local/lib/python2.6/dist-packages/Bio/GenBank/Scanner.py",
line 347, in _feed_feature_table
    consumer.location(location_string)
  File "/usr/local/lib/python2.6/dist-packages/Bio/GenBank/__init__.py",
line 975, in location
    raise LocationParserError(location_line)
Bio.GenBank.LocationParserError:
order(1078481..1078483,join(1078778,1078800..1078810))

The offending feature is:
misc_feature    complement(order(1078481..1078483,join(1078778,
                1078800..1078810)))
                /locus_tag="DKAM_1147"
                /note="active site"
                /db_xref="CDD:73252"

Could you look into whether this is a bug in the parser or in the input file?