[Bioperl-l] GFF feature start and end points on reverse strand

Lincoln Stein lstein at cshl.edu
Tue Feb 28 10:08:27 EST 2006


Call the absolute(1) method, which turns off relative addressing.

Lincoln

On Tuesday 28 February 2006 08:22, James Allen wrote:
> Hello,
> I'm retrieving data using the 'features' method of Bio::DB::GFF, and when
> the feature is on the reverse strand (ie = -1) the start and end points are
> flipped, so that 'feature->end' is the smaller number (ie what I consider
> the start point) and 'feature->start' is the larger number.
> Is there anyway to prevent this behaviour, so that the start value of my
> feature is the same as the start value in my database, regardless of the
> strand?
>
> Thanks,
> Julio
>
>
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Lincoln D. Stein
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