Fixes needed before we could do bulk validation

Hi GMOD,

(I'm offering this duplicate of https://github.com/tharris/gff3_validator/pull/1 made 2013-11-20 because I think the other has lost visiblity.)

Just offering some changes a colleague needed to make, before he could use this for bulk validation of some GFFs we have fetched or constructed.

Hope they're useful,

-- 
Matthew