Big Turkey break commit!

- Added __init__.py so metagenomics can be imported from other scripts
- Added a LOT of utility functions to metagenomics.py. They are all
thoroughly commented and have examples of usage.
- Commented perm_analysis.py more thoroughly and updated to be
consistent with changes in gpu_pssm and metagenomics.
- *NEW*: A (fully commented) parameters section!