[Biopython] gff3 problem

[Peter Cock]

On Tue, Apr 5, 2011 at 1:26 PM, Michal <mictadlo at gmail.com> wrote:
> Hello,
> I have found http://www.biopython.org/wiki/GFF_Parsing  for BioPython
> in order to read GFF3 files.

Oh good - I'm hoping to get down to using Brad's code myself, and
the more eyes on it now the better shape it will be in to merge into
Biopython.

> Why does start position is always one less than in the gff3 file, but
> the end position is the same?

That one I can answer, GFF3 using one-based counting, Python uses
zero based counting. Biopython parsers will covert into using Python
counting so that slicing etc works as expected within Python.
http://www.sequenceontology.org/gff3.shtml

Peter