moved all SQL queries into single Database module

It's all minor renaming and tweaks to get the names to line up.

The only more significant changes are in `gene`, `transcript`, and `exon`
where I switched out SQL queries for calls to `db.query`.

On Fri, Dec 12, 2014 at 4:05 PM, Tavi Nathanson <notifications@github.com>
wrote:
>
> In pyensembl/database.py
> <https://github.com/hammerlab/pyensembl/pull/16#discussion-diff-21773130>:
>
> > @@ -0,0 +1,298 @@
> > +from os.path import join, exists
>
> Nothing changed in this file, yes?
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/hammerlab/pyensembl/pull/16/files#r21773130>.
>