[BioPython] GenBank records again

[Peter Bienstman]

Try upgrading to the latest CVS version of BioPython. It has lots of GenBank 
fixes.

If that doesn't help, could you send us the GenBank record where the parser 
fails? It will be rather hard to debug otherwise ;-)

Peter 

On Thursday 27 February 2003 04:21, JINLING HUANG wrote:
> Jeff and all,
>
> Thank you very much for the GenBank record things. Now I am trying to
> retrieve protein sequences with a file of GenBank ids. My script is the
> following:
>
> from Bio import GenBank
> import sys
>
> file = sys.argv[1]
> fp1 = open(file, 'r+')    #file of gi
> ids = fp1.read()
>
> lids = ids.split()
> recNum = len(lids)
>
> protein_ncbi_dict = GenBank.NCBIDictionary(database='protein',
>                         format='gp', parser=GenBank.FeatureParser())
>
> for i in range(0, recNum):
>     gb_record = protein_ncbi_dict[lids[i]]
>     print '>'+ gb_record.id[0:-2] + '   ' + gb_record.seq.data
>
> The script works well most of the time, but sometimes it gives an error
> message:
>
> Traceback (most recent call last):
>   File "getGBRecords.py", line 25, in ?
>     gb_record = protein_ncbi_dict[lids[i]]
> File "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py",
> line 1563, in __getitem__ return self.parser.parse(handle)
>   File
> "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
> 268, in parse self._scanner.feed(handle, self._consumer)
>   File
> "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
> 1255, in feed self._parser.parseFile(handle)
>   File "/bio/python2.2/lib/python2.2/site-packages/Martel/Parser.py", line
> 338, in parseFile self.parseString(fileobj.read())
>   File "/bio/python2.2/lib/python2.2/site-packages/Martel/Parser.py", line
> 366, in parseString self._err_handler.fatalError(result)
>   File "/bio/python2.2/lib/python2.2/xml/sax/handler.py", line 38, in
> fatalError raise exception
> Martel.Parser.ParserPositionException: error parsing at or beyond character
> 14
>
>
> What is the reason for the problem? It seems that the problem is in the
> parser part, but I just don't know why.  Can anybody help?
>
> Best wishes,
>
> Jinling
>
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