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

Chris Fields cjfields at uiuc.edu
Tue Jun 26 10:02:29 EDT 2007


Ill try getting to that ASAP (as well as a few bugs).  The problem is  
we have to patch this in 2-3 places (SeqIO::swiss, SeqIO::embl) due  
to repeated code issues, something I'm trying to rectify with a new  
set of parsers.  Just haven't had the time to work on them lately  
unfortunately.

chris

On Jun 26, 2007, at 8:45 AM, Roy Chaudhuri wrote:

> 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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>>> Bioperl-l at lists.open-bio.org
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>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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