[Bioperl-l] Possible bug in Bio::SeqIO::embl.pm

Chris Fields cjfields at uiuc.edu
Tue Jun 26 09:13:50 EDT 2007


I can verify this using bioperl-live.  Can you file this as a bug?

http://bugzilla.open-bio.org/

chris

On Jun 26, 2007, at 2:05 AM, Jesper Krogh wrote:

> Hi List.
>
> Trying to parse the embl database, the embl-parser fails on: AB019196
> http://www.ebi.ac.uk/cgi-bin/expasyfetch?AB019196
>
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: AB019196 seems to have an invalid species classification.
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl/5.8/Bio/Root/Root.pm:359
> STACK: Bio::SeqIO::embl::_read_EMBL_Species
> /usr/share/perl/5.8/Bio/SeqIO/embl.pm:1091
> STACK: Bio::SeqIO::embl::next_seq
> /usr/share/perl/5.8/Bio/SeqIO/embl.pm:322
> STACK: -e:1
> -----------------------------------------------------------
>
>
> It seems to be dissatisfied with this:
> OS   Acetobacter aceti
> OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
> OC   Acetobacteraceae; Acetobacter; Acetobacter subgen. Acetobacter.
>
> Thanks.
> -- 
> Jesper Krogh
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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