[Bioperl-pipeline] Genewise matters(start,stop modification)
Shawn
shawnh@fugu-sg.org
11 Sep 2002 06:46:43 +0800
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