[BioPython] Cannot parse ApE plasmid editor GenBank file

[Martin MOKREJŠ]

Hi,

Martin MOKREJŠ wrote:
> Hi Peter, I have re-tried current CVS version of biopyhton with a
> file regenerated by fixed version of ApE editor. Unfortunately, I
> got:
> 
> $ python generate_image_from_genbank.py Traceback (most recent call
> last): File "generate_image_from_genbank.py", line 7, in ? 
> genbank_entry = parser.parse(fhandle) File
> "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line 187,
> in parse self._scanner.feed(handle, self._consumer) File
> "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py", line 360,
> in feed self._feed_first_line(consumer, self.line) File
> "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py", line 876,
> in _feed_first_line raise SyntaxError('Did not recognise the LOCUS
> line layout:\n' + line) SyntaxError: Did not recognise the LOCUS line
> layout: LOCUS       pBL-RLuc-GBB+3-III        5391 bp ds-DNA
> circular 14-JUN-2007
> 
> What's wrong with the LOCUS line now? Bioperl from CVS can read it,
> and I thought it is already following the current specs. ;-) Thanks
> for your help, Martin

OK, I have found the spacing problem with my LOCUS lines still to persist,
and after some scripting I got the lines fixed. Now I get with current CVS
version:

$ python generate_image_from_genbank.py 
Traceback (most recent call last):
  File "generate_image_from_genbank.py", line 7, in ?
    genbank_entry = parser.parse(fhandle)
  File "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line 187, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py", line 361, in feed
    self._feed_header_lines(consumer, self.parse_header())
  File "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py", line 978, in _feed_header_lines
    consumer.taxonomy(data.strip())
  File "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line 419, in taxonomy
    self.data.annotations['taxonomy'] = self._split_taxonomy(content)
  File "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line 250, in _split_taxonomy
    if taxonomy_string[-1] == '.':
IndexError: string index out of range
$

The file starts with:

LOCUS       pBL-RLuc-GBB+3-III      5391 bp    ds-DNA  circular SYN 14-JUN-2007
DEFINITION  .
ACCESSION   .
VERSION     .
SOURCE      .
   ORGANISM  .
COMMENT     
COMMENT     ApEinfo:methylated:0
FEATURES             Location/Qualifiers