[Bioperl-l] new directions

[Ewan Birney]

On Thu, 8 Mar 2001, Jason Stajich wrote:

> 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?

I view Bio::Index as an implementation of Bio::DB interfaces. Bio::Index
are write-once, read-many, not really read-write

It would have probably been better to put Bio::Index in Bio::DB::Index. Oh
well...

> 
> 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.
> 

;) Yup. I know how to do that!

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

Indeed.


> -Jason
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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