[Bioperl-pipeline] runnable parameters

[Elia Stupka]

> ok will give it a shot. everything is up for review once we get the annotation
> pipeline thru.

Then I *AM* taking you guys out for a hell of a meal! :)

> hmm. maybe we can talk about this tomorrow. You are talking about
> in-memory stuff?

Just basically saying that right now you are dealing with how you map
coordinates of genes coming out of genewise, and all I was trying to say
is that if you have fed a fake miniseq to genewise, the calculation will
not be a simple offset+start, offset+end, but will depend on the offset of
each sub_SeqFeature that was miniseq'ed and how much padding was
applied... the code is all there in the ensembl runnabledbs, all I am
asking is whether you think your current design can accomodate it, since
the information needed for the mapping is more complex.

> What do u mean de-mini-seq ing? to combine the exons in to a transcript ?

No, I want to make sure we are on the same page here, so here is an
example:

protein A hits human chr 1 at bps 100-200 and 1000000-1000400 (typical
case in human, introns can be a megabase)

Exon padding set to 50 base pairs.

So you cut chr1 from 50 to 250, and from 999050 to 1000450, and stitch
them into a miniseq that is 700 base pairs long.

Then you feed the protein and miniseq to genewise. Genewise produces a
gene with two exons (in miniseq coordinates):
exon 1: 30-170
exon 2: 230-670

These need to be converted back to chr1 coordinates, i.e. add 50 offset to
the exon 1 coordinates, and add 999050 to the exon2 coordinates, thus
getting the real coordinates

exon 1: 80-220
exon 2: 999080-1000420

Finally you can store the gene....

Having explained it all I realise that all you need to allow is to be able
to feed more than one offset (and the strand) to do the conversion
compared to what you are doing now, so it's not a big deal and we might
want to fix it and test it sooner rather than later...

Fiuuu that was a long numbery mail ;)

Elia

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