[Bioperl-l] LocatableSeq NSE format - suggested changes

Mark A. Jensen maj at fortinbras.us
Wed Dec 16 07:51:24 EST 2009

I'm with Dave; option 1 is cleaner. The only problem might be the automatic 
interpretation of older output as always plus strand, but presumably these would 
have had to record the strandedness explicitly elsewhere, so they would be 
updatable. I'm definitely for making strandedness part of the spec in some way. 
cheers MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Monday, December 14, 2009 8:23 PM
Subject: [Bioperl-l] LocatableSeq NSE format - suggested changes

> All,
> The current output for NSE format (Name/Start-End) via 
> Bio::LocatableSeq::get_nse() currently doesn't allow for strandedness.  I have 
> seen two variations of NSE that incorporate strandedness:
> 1) Stockholm Rfam reverses start and end if the strand == -1
>   chrY/598-1
> 2) Sheldon McKay's Gbrowse_syn uses Name(strand)/start-end
>   rice-3(+)/16598648-16600199
> The former breaks fewer things within BioPerl, but the latter seems more 
> explicit.  Any preferences?  Do we want a new method that creates this, and 
> deprecate out simple non-stranded NSE?
> chris
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