[Biopython-dev] EMBL flatfile parsing

Peter (BioPython-dev) biopython-dev at maubp.freeserve.co.uk
Wed Apr 12 20:13:52 UTC 2006

Albert Krewinkel wrote:
> Hello,
> I am trying to parse a EMBL-formated file with biopython, but I
> couldn't find any working parser for this. When I try to use the
> Martel-based parser as described in one of the mailinglist-threads, I
> get the following error:


> Martel.Parser.ParserPositionException: error parsing at or beyond character 0
> The file itself appears to be okay, since it can be read by 'seqret'
> and bioperl. This seems to be a parser problem -- or am I doing
> something wrong?

This does sound like there may have been a file format change, and it no 
longer matches what BioPython is expecting.

Could you log a bug (based on your previous email), and attach an 
example EMBL file.  Or email it directly to me.



P.S. Sorry for the delay in my reply - I was hoping someone familiar 
with EMBL would step forward...

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