[Biopython-dev] need help with Genbank

[Jeffrey Chang]

The GenBank parser has gone through a few revisions to handle format
changes since 1.00a4 was released.  Try getting the latest version out
of CVS (cvs.open-bio.org) and see if that fixes the problem.

Otherwise, please send in a sample GenBank record that causes the
parser to break.

Jeff




On Thu, Jul 18, 2002 at 11:02:41AM -0500, Dinakar Desai wrote:
> Hello:
> 
> I have install biopython1.004a and python 2.2.1 on linux box. I am going 
> through tutorial written by Brad et al. (very good work).
> With following code I get trace back which I have pasted at the end.
> Can someone help me with.  I must be dong something wrong here.
> 
> Thanks
> 
> Dinakar
> <code>
> 	30 from Bio import GenBank
>       31 record_file = open('record_file.seq', 'w+')
>       32 record_parser = GenBank.FeatureParser()
>       33 ncbi_dict = GenBank.NCBIDictionary()
>       34 for id in titles:
>       35   gb_seqrecord = ncbi_dict[id]
>       36   record_file.write( gb_seqrecord)
>       37
>       38
>       39 record_file.close()
>       40 record_file = open('record_file.seq', 'r')
>       41 gb_iter = GenBank.Iterator(record_file, record_parser)
>       42 while 1:
>       43   current_record = gb_iter.next()
>       44   if current_record is None:
>       45     break
>       46   print current_record.seq
>       47   print current_record.source
>       48   print current_record.author
>       49 record_file.close()
> 
> </code>
> <traceback>
> Traceback (most recent call last):
>    File "./test_as.py", line 43, in ?
>      current_record = gb_iter.next()
>    File 
> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linet
>      return self._parser.parse(File.StringHandle(data))
>    File 
> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linee
>      self._scanner.feed(handle, self._consumer)
>    File 
> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", lined
>      self._parser.parseFile(handle)
>    File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", 
> line 230, ie
>      self.parseString(fileobj.read())
>    File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", 
> line 258, ig
>      self._err_handler.fatalError(result)
>    File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in 
> fatalError
>      raise exception
> Martel.Parser.ParserPositionException: error parsing at or beyond 
> character 55
> 
> </traceback>
> -- 
> 
> 
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