[Bioperl-l] sim4 parser?

[Hilmar Lapp]

That's a good point. It actually returns 
Bio::SeqFeature::Gene::ExonI implementing objects, right? We don't 
want to miss that I guess ...

	-hilmar

On Wednesday, August 21, 2002, at 05:21  PM, Jason Stajich wrote:

> 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
>
>
--
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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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