[Bioperl-l] LocatableSeq NSE format - suggested changes

Chris Fields cjfields at illinois.edu
Mon Dec 14 20:23:05 EST 2009


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

2) Sheldon McKay's Gbrowse_syn uses Name(strand)/start-end


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?


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