[Bioperl-pipeline] runnable parameters

[shawnh@worf.fugu-sg.org]

Hi Guys,
	was thinking a little about this. You will be surprised
how many design stuff crops up while trying to run one simply genewise.
But its for the best...

We have arguments for the following

I/O Handlers(static and dynamic)
Input_create
Filter


Turns out we might need arguments for runnables as well.
This is not just the parameter argument which is known at run time.

This is due to some issues with genewise. There maybe another solution
which doesn't require this but I can't think of a good one.
I'm using get_Virtual_Contig_by_chr_start_end to fetch a sequence
and passing it to the genewise runnable. Lacking in this set of information 
are contig_id and the chromosomal coordinates.

>From my view, a generic solution to work with the genewise runnable is 
to allow the runnable to take in arguments mainly:
1) Bio::Location
2) Seqname

these arguments are generated by input create of course.

Thus in addition to the analysis parameters in the analysis table, this
will be merged with the arguments above. The runnable will then do the coordinate
mapping, set some tag value for the seqname and this bioperl gene object is then
passed to some bioperl-ensembl converter before sent for storage.


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'


hmmm yet another schema change.

better leave this for tomorrow.

shawn



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