Bioperl-guts: Thoughts on GeneBank location descriptors

Ewan Birney birney@sanger.ac.uk
Tue, 24 Aug 1999 15:18:40 +0100 (BST)


On Tue, 24 Aug 1999, Zia Khan wrote:

> For one of my GeneBank related features, I'm adding support or
> GeneBank/EMBL style feature location descriptors (not simply start and
> end). Has there been any discussion on the list on how to go about dealing
> with them? I have some code worked out (yet to be debugged arrgh...). That
> allows you to extract spans of sequence based on these location
> descriptors (join(), complement(), order(), 23..3828, etc.).

Zia -

The SeqFeature system that is currently in place on the cvs head handles
it as follows:

	a join(xx,yy,zz) maps to 

	a seqfeature(start = xx.start, end = zz.end) 
		with subseqfeatures at
			(xx.start,xx.end),
			(yy.start,yy.end),
			(zz.start,zz.end)

The benefit of this system is that we can provide a decent representation
using "simple" ranges of these complex features.

This scheme is mapped out in the AnnSeqIO/FTHelper code. I would strongly
recommend you browse around the AnnSeqIO/EMBL.pm and AnnSeqIO/FTHelper
code to see how I wrote it with the EMBL feature table. The FTHelper
module should be reused in the (putative) AnnSeqIO/GenBank.pm module,
which we haven't written yet, but someone at the EBI is planning to have
a stab at.


I am rather worried that your work is not dovetailing with the AnnSeq
and AnnSeqIO system, which would mean we would have two different ways
of representing features in the Bioperl package, which would be bad news.
Can you send the guts list an outline of what you have been doing? Or
possibly send hte list or me the code you have been working on? This
way we can figure out how it can fit in. I don't want to have to spend
a while untangling your stuff or changing my stuff because we didn't talk
things through clearly beforehand.


But it is great that you are doing this. Keep it up!



> 
> Zia Khan
> Carnegie Mellon University
> zkhan@andrew.cmu.edu
> 
> 
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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