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

Roy Chaudhuri rrc22 at cam.ac.uk
Tue Jun 26 09:45:01 EDT 2007


Sorry, replied to this but forgot to cc the list.

It looks like a related problem to bug 2288 that I filed about 
Bio::SeqIO::swiss - the period after subgen. is what causes the problems 
since it is interpreted as a seperator between nodes. I put a patch in 
for Bio::SeqIO::swiss that works for me, but I guess it might have side 
effects.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

Chris Fields wrote:
> 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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