[Bioperl-l] sim4 parser?

[Jason Stajich]

I already did HMMER - rewrote it so it doesn't depend on
Tools::HMMER either - we may still want to retain Tools::Sim4 since it
would provide gene centric interface while SearchIO would be Hit/HSP
centric -- unless we want to build some methods into a
Search::Hit::Sim4Hit which would return a gene model object which might be
a good idea??

Rambling here  ... We should probably consider a SearchIO for Est2Genome?

A Genewise parser might be reasonable some day too, but I'm just
suggesting things to those sitting on their hands looking for little
coding projects -- the biggest issue is the gene model objects aren't
really matured just yet so some work would need to be done to those.

-jason

On Wed, 21 Aug 2002, Hilmar Lapp wrote:

> That'd be really great. The Sim4 parser and the HMMER parser are I
> believe on the list of parsers to be migrated to SearchIO.
>
> If you need any explanation on how it works internally let me know,
> but that was all a while ago ... Shouldn't be too hard to figure,
> but everyone claims that :)
>
> 	-hilmar
>
> On Wednesday, August 21, 2002, at 10:10  PM, Chris Mungall wrote:
>
> > oh, duh, i've just found it, sorry. should i convert it to SearchIO?
> >
> > On Wed, 21 Aug 2002, Chris Mungall wrote:
> >
> >> wasn't there a sim4 parser once?
> >>
> >> should i write one from scratch?
> >>
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> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu