[Bioperl-pipeline] runnable parameters

[Elia Stupka]

> 	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...

;) That's what I expected... though I think blast-to-genewise (at the
moment) covers one of the most annoyingly complicated issues we will face
for a while...

hmmm... I've read your mail and I am a bit lost (probably because it's
over e-mail at night and while I am doing all the slides for tomorrow)...

...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?

> 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

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