Initial commit of messy code, specific to microbiomic data.
Merge pull request #2 from rybern/master

Initial commit of messy code, specific to microbiomic data.
Added a script command line and settings file interface, starting to refactor code
Added flexiblity (nothing is now specific to microbiomic data)
Added functionality (feature vector reporting)
Refactored some of the more complex parts
Removed outdated sections

Not yet ready for use. Still need to finish documentation and refactoring sections.
removed old file
Added documentation
Added plot.py, added file support, added testing (without test partition), added minerva results, added minerva scripts (previous run)
Merge pull request #3 from rybern/code-cleanup

Code cleanup