Add simpler option for function type selection

Adds '-t, --type_of_prediction' option to predict_metagenomes.py,
so user can easily specify whether they want 'KO' or 'COG' predictions.
User can still explicitly specify the precalculated file using the previous '-c' option.

Fix #118

Also, added and clarified some of the usage documentation and verbose statements.
Merge pull request #119 from mlangill/issue118

Adds more user-friendly option for specificying function type