[Bioperl-l] new directions

[Jason Stajich]

On Wed, 7 Mar 2001, Chris Mungall wrote:

> 
> On Wed, 7 Mar 2001, Jason Stajich wrote:
> 
>   
> >  o Bio::Index::Blast which can read fetch ( and store?) seqs from a blast
> >    index.
> 
> you mean using the .nsq files or whatever they are to do random-access of
> a fastafile to pluck out your seq of interest?
> 
> I already have a perl module for random access of fasta files (we
> occasionally use fasta files with ~20mb entries and it's useful to be able
> to snip out a couple of kb from right in the middle of the entry), I'll
> happily donate this to bioperl. 
> 
yes this would be awesome - If you are willing to donate it, we either
need to put it in Bio::DB or Bio::Index.  I can never decide how these
should work - are Bio::DB's read-only while Bio::Index's are R/W?

Anyways, if you don't have time to make it subscribe to the necessary
interfaces, I'm happy to do it, just let me know.  If you want to donate
the perl code first and then see about adding the C-extensions later, that
would be a great.  Ewan can probably give some pointers on how we should
name things so the c-extension gets picked up when installed but otherwise
the perl-only code runs.

Convention is perl-only code in bioperl-live and c code in bioperl-ext.

-Jason
Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/