[BioPython] Biopython GenBank

[Jeffrey Chang]

This means that there is something in the GenBank record you are
trying to parse that the parser does not handle.  Are you using
Biopython 1.00a4 or the files from CVS?  The formats change faster
than we make biopython distributions, so you should try getting the
appropriate GenBank files from CVS and see if that fixes your problem.

Jeff




On Tue, Nov 19, 2002 at 09:25:25AM -0500, JINLING HUANG wrote:
> Hello,
> 
> I am writing a script to parse GenBank records using biopython.
> Essentially I just copied the script from the biopython tutorial as
> follows:
> 
> from Bio import GenBank
> 
> gb_file = 'ncbiSamples'
> 
> gb_handle = open(gb_file, 'r')
> fp1 = open('ncbiSeq', 'w+')
> 
> feature_parser = GenBank.FeatureParser()
> 
> gb_iterator = GenBank.Iterator(gb_handle, feature_parser)
> 
> while 1:
>     cur_record = gb_iterator.next()
>     if cur_record is None:
>        break
>     print cur_record.id
>     sequence=cur_record.seq.data
>     print sequence
>     fp1.write('>'+cur_record.id[:-2]+'\n'+sequence+'\n')
> 
> 
> The script worked well for some records. The I got error messages:
> 
> Traceback (most recent call last):
>   File "getSeq.py", line 13, in ?
>     cur_record = gb_iterator.next()
>   File "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
>     183, in next return self._parser.parse(File.StringHandle(data))
>   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
>     1252, 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 1525
> 
> 
> Has everyone encountered the same problem? How do we get rid of this
> problem?
> 
> Best wishes,
> 
> Jinling Huang
> 
> 
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