[BioPython] problem with GenBank.NCBIDictionary ?

[Catherine Letondal]

Cath Lawrence wrote:
> On Wednesday, May 29, 2002, at 02:25 AM, Catherine Letondal wrote:
> > If I change the parser to be either the GenBank.RecordParser or the 
> > GenBank.FeatureParser
> > as shown in the tutorial, I get a Martel error message.
> ...
> > Martel.Parser.ParserPositionException: error parsing at or beyond 
> > character 55
> > Could someone help?
> 
> Yup, I had this when I started with BioPython last month.
> 
> This is the LOCUS line change (it doesn't like seeing "linear").
> Grab the latest version from CVS and it should be fine.

The latest version from Bio/GenBank/__init__.py ? I have downloaded
the latest CVS version, but I still get exactly the same error as soon as 
I try to use either the GenBank.RecordParser() or the GenBank.FeatureParser() ??

gb_dict = GenBank.NCBIDictionary(parser = GenBank.RecordParser())
gb_record = gb_dict['180255']

Traceback (most recent call last):
  File "exemples/gb_refs.py", line 56, in ?
    gb_rec = search_gbrec(ref)
  File "exemples/gb_refs.py", line 48, in search_gbrec
    gb_record = gb_dict[gi_list[0]]
  File "/local/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1557, in __getitem__
    return self.parser.parse(handle)
  File "/local/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 289, in parse
    self._scanner.feed(handle, self._consumer)
  File "/local/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1252, in feed
    self._parser.parseFile(handle)
  File "/local/lib/python2.2/site-packages/Martel/Parser.py", line 230, in parseFile
    self.parseString(fileobj.read())
  File "/local/lib/python2.2/site-packages/Martel/Parser.py", line 258, in parseString
    self._err_handler.fatalError(result)
  File "/local/lib/python2.2/xml/sax/handler.py", line 38, in fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond character 55

(although:
gb_dict = GenBank.NCBIDictionary()
gb_record = gb_dict['180255']

works perfectly)


Or do you mean the latest version of Martel/Parser.py? (since the error seamed
to be more at this step). I have also downloaded the latest version, but
in this case, I get another error:

Traceback (most recent call last):
  File "exemples/gb_refs.py", line 4, in ?
    from Bio import GenBank
  File "/local/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 53, in ?
    import Martel
  File "/local/lib/python2.2/site-packages/Martel/__init__.py", line 6, in ?
    import Expression
  File "/local/lib/python2.2/site-packages/Martel/Expression.py", line 31, in ?
    import Parser
  File "/local/lib/python2.2/site-packages/Martel/Parser.py", line 40, in ?
    import Dispatch
ImportError: No module named Dispatch
>>> 

Thanks for any help,

--
Catherine Letondal -- Pasteur Institute Computing Center