[Biopython-dev] need help with Genbank

[Dinakar Desai]

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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