[Bioperl-pipeline] runnable parameters

[shawnh@worf.fugu-sg.org]

> 
> 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.

ah I see ...

> 
> 
> 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

so if the exon 1 goes in to the other 2nd mini-seq part, u must adjust.
ok..doable.

> 
> 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...


yup the genewise runnable should do the trick. however its debatable how inflated
we want the runnable to be..but of course the initial design to have runnables
as modules is to allow for things like this.

I guess we will pass in the start/end/ info as cigar strings. hm. yup. sounding more doable.

ok..off to bed. good nite!


shawn





> 
> Fiuuu that was a long numbery mail ;)
> 
> Elia
> 
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