[BioPython] parsing error with GenBank.RecordParser

[Hans Meier]

 Hi,
 
 parsing of NC_000913.gbk does not work.
 
 
 Greets, Harald
 
 
 ***********************************************
 >>> from Bio import GenBank
 >>> parser = GenBank.RecordParser()
 >>> record = parser.parse(open('NC_000913.gbk'))
 
 Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/usr/lib/python2.3/site-packages/Bio/GenBank/__init__.py", line 240,  
   in parse self._scanner.feed(handle, self._consumer)
   File "/usr/lib/python2.3/site-packages/Bio/GenBank/__init__.py",line1259,
   in feed  self._parser.parseFile(handle)
   File "/usr/lib/python2.3/site-packages/Martel/Parser.py", line 328,
   in parse File self.parseString(fileobj.read())
   File "/usr/lib/python2.3/site-packages/Martel/Parser.py", line 356, 
   in parseString self._err_handler.fatalError(result)
   File "/usr/lib/python2.3/site-packages/_xmlplus/sax/handler.py", line 38,
   in fatalError raise exception
   
  Martel.Parser.ParserPositionException: error parsing at or beyond  
  character 856717
 *************************************************
 
 Beyond character 856717 comes the following:
 
/note="2'-(5"-phosphoribosyl)-3'-dephospho-CoA
transferase; holo-citrate lyase synthase; CitG forms the
prosthetic group precursor
2'-(5"-triphosphoribosyl)-3'-dephospho-CoA which is then
transferred to apo-ACP by CitX to produce holo-ACP and
pyrophosphate;
go_process: protein modification [goid 0006464]"
 
 
 
 

		
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