[Bioperl-l] Request for comments: Bio::DB::GFF3 namespace

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Mar 30 17:37:30 EST 2006


Lincoln,

> I'm pretty much ready to check in the replacement for the Bio::DB::GFF 
> database. What I ended up writing has only a remote relationship to gff3 
> files -- it is more like a general storage engine for Bio::SeqFeatureI 
> objects. So I don't want to call the thing Bio::DB::GFF, but want to place it 
> somewhere else in the namespace hierarchy.
> 	Bio::SeqFeature::Store
> 		- implements the Bio::SeqFeature::CollectionI interface. You can
> 		store any Bio::SeqFeatureI into a database (mysql, berkeleydb, in-memory)
> 		and fetch it out using a variety of queries.
> A utility script, currently called gff3_load.pl, parses a gff3 file, creates 
> the proper objects, and stores them in the Store. Eventually some of this 
> functionality will be moved into Bio::Tools::GFF.

Is the focus still only on bulk loading + searching?
ie. mainly read-only activites like with gbrowse?

Or is dynamic inserting + writing also well supported?
ie. could be used as a persistent Bio::SeqFeatureI object store.

How do you see this module in relationship to the BioSQL project?

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/


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