[Bioperl-l] Bio::Tools::GFF GFF3 parsing

[Jason Stajich]

I added support for GFF3 parsing to Bio::Tools::GFF and added some simple
tests.  I'm not 100% I have GFF3 output correct so Chris Mungall, Lincoln
if you don't mind giving it a look over that would be great.  If I've
duplicated functionality from somewhere else let me know, but I think
Bio::Tools::GFF needs to be able to parse in GFF3 format at some point.

The GFF3 parsing seems to work fine for processing the BGDP annotations so
I feel confident it is working correctly, but more testing is welcomed!

This is no real support for Unicode type output, the simpliest solution
would be to rely on HTML::Entities for encoding non-ASCII codes.  I wasn't
sure I wanted to make Tools::GFF depend on this right now so I've just
implemented a simple encoding for '=,;'.  Feel free to fix this if it
needs to be more aggresive.

-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu