Remove dependency on ptools.

ptools was broken on Ruby 1.9.2 sometime back. Turns out the fix breaks ptools
on 1.8.7.

I think we can get by without File.binary? from ptools, relying instead on
DatabaseFormatter#probably_fasta?. The overhead should roughly be the same.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>