[Bioperl-pipeline] Genewise matters(start,stop modification)

[Shawn]

On Tue, 2002-09-10 at 13:07, Elia Stupka wrote:
> > I'm currently working on the DataMonger for genewise. 
> > A solution for coordinate mapping.
> 
> Just a thought, shouldn't we just use a CoordinateMapper object that can
> be reused all over the place (Heikki wrote one)?

will take a look. Note sure where to slot it in, prior to storing?


> > Bio::Pipeline::InputCreate::setup_genewise (setups input,job,dynamic
> > argument tables etc)
> 
> Just wondering, is this one mega-InputCreate object which will keep
> accumulating more and more method calls? Shouldn't we have one object per
> hack we want to get done? Also, isn't setup_genewise too generic because
> we might need to "setup_genewise" from other arguments?

No, I have InputCreate as a SeqIO type module where u plug in different 
inputcreate objects.Same for Filter.

setup_genewise isn't really complicated. All it does is extract
contig start,end and protein_hid

takes in 2 iohandler ids,

with that info, create two inputs and jobs
and store.


what other arguments are u thinking about?

there is also gonna be input_create objects for setting up pipeline from
scratch, different permutations etc.

 
> 
> I will finish off the DasAdaptor for GFD, Lincoln finished his (of
> course) did you see?
> 
> I think in the end we might want to support both BioSQL+GFD -> gBrowse as
> well as GFD(biosql,ensembl,files) -> gBrowse...


ok

shawn