[Biopython-dev] EMBL flatfile parsing
Peter (BioPython-dev)
biopython-dev at maubp.freeserve.co.uk
Wed Apr 12 16:13:52 EDT 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.
Thanks
Peter
P.S. Sorry for the delay in my reply - I was hoping someone familiar
with EMBL would step forward...
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