[Bioperl-l] Caching sequences

Jason Stajich jason at bioperl.org
Fri Oct 27 11:38:05 EDT 2006


Bio::DB::FileCache does one better and lets you cache the data in a
persistent file.  Not sure this index is shareable among users though -
bioperl-db is a better soln when that is desired.

-jason

On 10/27/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> > I have a script that is capable of downloading sequences from GenBank
> > based on GI numbers. I retrieve them if fasta format in order to save
> > bandwidth, but I'd like to take this one step further and cache the
> > sequences in case the user want to rerun the script using some of the
> > GI's they used previously.
> >
> > Does anyone have any guidance on how best to do this?
> >
> > Cheers
> > Nath
>
> There is Bio::DB::InMemoryCache, which is really an interface but appears
> to
> have several methods defined; you could look for modules which implement
> it.
> Sendu's suggestion of the Bio::Index modules and bioperl-db are also good
> starting points.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
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>



-- 
Jason Stajich
jason at bioperl.org
http://www.duke.edu/~jes12/


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