[Bioperl-l] Why does Bio::DB::GFF::Feature::gff3_string swap start and stop coordinates??

Chris Fields cjfields at uiuc.edu
Tue May 8 17:12:45 UTC 2007

I believe all seqfeature location coordinates are designed to have  
start < stop for consistency; in cases where the strand matters (CDS,  
gene, etc.) then the strand is set to 1 or -1.  When start > stop,  
the two are reversed and the strand is flipped; at least that's the  
way locations are set up in BioPerl.


On May 8, 2007, at 11:59 AM, Cook, Malcolm wrote:

> Why does Bio::DB::GFF::Feature::gff3_string swap start and stop
> coordinates,
> as in:
>   ($start,$stop) = ($stop,$start) if defined($start) && defined($stop)
> && $start > $stop;
> I thought it is not legal for a feature to be so composed.
> Anyone know?
> Cheers,
> Malcolm Cook
> Stowers Institute for Medical Research - Kansas City, Missouri
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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