[Bioperl-l] Bio::SeqFeature::Annotated and mandatory type checking

Scott Cain cain at cshl.edu
Fri Dec 15 00:01:36 EST 2006


As much as I would like to take credit for this :-)  Allen Day wrote the
original code, and then Chris Fields tried to fix it so that it actually
worked :-)  I think it would be a good idea to have a validate_terms
option like Bio::FeatureIO::gff.

Scott

On Thu, 2006-12-14 at 17:15 -0500, Sendu Bala wrote:
> Matthew Vaughn wrote:
> > Dear all,
> > 
> > I'm trying to bring some of my code into compliance with the BioPerl 
> > 1.5.2 and am running into some design decisions that I am unclear on. 
> > Can I ask why Bio::SeqFeature::Annotated enforces mandatory checking of 
> > the 'type' against SOFA? It seems to me that this should be optional 
> > behavior as is the case with the Bio::FeatureIO family. I'd be happy to 
> > write the patch if there is any agreement with me on this case.
> 
> Lots of people seem to have worked on it over the years, but perhaps 
> Scott Cain is the person to talk to?
> 
> revision 1.4
> date: 2004/09/25 11:41:29;  author: scain;  state: Exp;  lines: +1 -1
> two things:
>    * adding SOFA as an available ontology to DocumentRegistry.pm
>    * modifying FeatureIO::gff to use SOFA to validate, and to parse 
> Ontology_term
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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