[Bioperl-l] Database Retrieval

Sean Davis sdavis2 at mail.nih.gov
Tue Aug 8 13:14:04 EDT 2006




On 8/8/06 12:53 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> Sounds good.  I guess first things first.  We should get the basic
> UCSC DB backend up and running first, then implement RandomAccessI
> for simple sequence retrieval.  I'll try getting interfaces for
> Location, Refs, others along the way, which can be implemented as
> needed.  This will be pretty simple
> 
> So, we'll probably have something along the lines of
> 
> Bio::DB::RandomAccessI - Bio::SeqI retrieval interface
> Bio::DB::LocationI - Bio::LocationI retrieval interface
> Bio::DB::ReferenceI - Bio::Annotation::Reference (or similar)
> retrieval interface
> Bio::DB::ClusterI - Bio::ClusterI retrieval interface (SNP)
> ....and so on
> 
> Should Sean get an CVS account or should we just pass everything via
> a proxy, Sendu maybe?  Might be easier to give him CVS access so
> Sendu can focus on Taxonomy, I can focus on the interfaces and
> getting through my benchwork (?!?), and Hilmar can focus on $job.

Whatever works for me, although I should probably run stuff by folks first,
as I'm not used to the bioperl conventions--errors, etc....

Sean



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