[Bioperl-pipeline] runnable parameters

[shawnh@worf.fugu-sg.org]

> ...anyway, why couldn't the output come out with "mini" coordinates, and
> be passed to a datamonger that does the coordinate mapping based on the
> coordinates of the inputs for the previous job?

Right now, DataMonger isn't tied to analysis.
ok so if we are spawning a DataMonger job for mapping, then it will have to know what
the inputs of the previous job. Thus I guess, we need to create a new data monger job
with arguments and inputs from the previous job and interprete those arguments
appropriately. Just wondering whether its tricky
to setup this job. Whether we need an input_create for an input_create ...
Doable..just a little hacky for me. I figured passing parameters to runnables
aren't a isolated affair. At the same time, its not insane for Genewise runnable to do 
coordinate mapping. But then again mapping maybe something worth generalizing into a
data monger. hmm.
ok. I will see if I can write up the latter.


shawn



> 
> > The alterative and maybe I'm not too familar with VirtualContigs is to
> > have the genewise runnable take in SeqFeatures and get the attached
> > seq. But this makes the runnable a tad strict I think. Also, I'm not
> > sure how to fetch this 'seqfeature'
> 
> You can attach sequences very easily by getting a feature and doing
> attach_seq and then the sequence object that is underlying it, but it's a
> suicidal solution because you end up shifting around huge sequences...
> 
> Elia
> 
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 6874 1467        *
> * mobile: +65 9030 7613        *
> * fax:    +65 6779 1117        *
> ********************************
> 
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************