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

[Elia Stupka]

> 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)?

> prolly makes sense only for kiran and elia but in anycase, we will need
> to code review this. 

So far it all makes sense and follows our discussions.

> 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?

> Question, for ciona, what is the method call for getting the contig
> slice?
> fetch_VirtualContig_by_chr_start_end
> we need a static_golden_path for this I reckon?

The static_golden_path is loaded in, check with Bala, I think he loaded it
in a test database rather than the live one to be on the safe side.

> the other thing to be done is implementing the converter functionality
> tied with IOHandlers.

You mean SeqFeatureIO right? Yep...

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...

Elia

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