[Bioperl-l] storing and retrieving partial sequences

[Jason Eric Stajich]

There is the capability for getting a subseq in the bioperl-db
implementation (bioperl layer on top of mysql).  We don't currently cache
anything though so each subseq requires a new db call.  However, there
should be capability there to build your own Bio::Seq::CachingSeq which
intercepts calls if need be.

Not sure I totally understand the scenario so not sure if this helps.

-jason

On Mon, 3 Dec 2001, Jonathan Epstein wrote:

> Hi,
>
> Does anyone have a good BioPerl or ACEDB way to handle storing and
> retrieval of partial sequences?
>
> The idea is that, say, I might have bp 50001-100000 of a particular
> sequence which is 500kb long.  I want to cache this local result,
> since obtaining the other sequence data may be computationally very
> complex and may even require manual intervention.  So, if subsequently
> there is a query for bp 56000-60000 I want to retrieve the data
> immediately from the local cache.  If there is a query for bp
> 40000--60000 I want to retrieve the cached portion of the data, and
> set in motion whatever is needed to obtain the missing data.
>
> For now we are starting a home-grown mySQL solution, but I really
> prefer to use a solution which is BioPerl-based or at least
> BioPerl-like.
>
> Can anyone suggest how we might hook into Bio::DB or Bio::Seq or ... ?
>
> Thanks,
>
> - Jonathan
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu