[Bioperl-l] order of sublocations

[Marc Logghe]

> -----Original Message-----
> From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
> Sent: Wednesday, September 17, 2003 2:18 PM
> To: Marc Logghe
> Cc: Bioperl-L (E-mail)
> Subject: Re: [Bioperl-l] order of sublocations
> 
> 
> This alone won't work because of the case when we have remote 
> locations
> the sorting will mess up that order.  Besides the order specified does
> mean something - we had to go through this with the 
> spliced_seq method to
> generate the spliced out sequence.
> 
> If we're specifying a gene on the complement it would be 
> incorrect to sort the
> exons like you have shown - that puts them in the wrong order.

I don't know whether there is a concept of 'wrong order', is there ?. Is it relevant in Bioperl ?
Nothing is said about it in the Feature Table Definition. You can only notice that in the examples they give, the sublocations are nicely sorted.
I was just reasoning: if it is not relevant for Bioperl why not just sort them, even when they end up 'wrongly sorted' ;-)


> Perhaps complement(join(<1..66,129..218)) is what VectorNTI 
> wants - but
> we've been down that road before in getting the code to 
> output this and
> it would require doing something a bit different to distribute the
> complementation status to all the subfeatures.
> 
> To please VectorNTI it seems to me we need to split CDSes 
> into individual
> exons - if this is in regard to SequenceDumping in Gbrowse - I have a
> 'CDS' track which I use to dump the CDSes as individual 
> features rather
> than joined together.
Like I said: it is more a VectorNTI problem.
I preferred to have a CDS in stead of exons because the picture looks less messy. When you have to deal with exons of different splicing variants, you can't easily see which exons belong to each other. It is pic1 versus pic2.
Cheers,
Marc
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