[Bioperl-l] LocatableSeq NSE format - suggested changes

[Chris Fields]

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