fixed index
Cleanups and refactoring

* Only do one check for output_directory by combining statements
* rename output to number_of_reads
* get rid of useless comment
do the matrix rotations and manipulations in quikr_train instead of quikr
removed debugging statements
Check if file is compressed
added gzip compression support
multifasta_to_otu.py support for compression
minor formatting cleanup
starting to modularize
fix multifasta_to_otu
fix quikr
convert into a module, rename out functions so all quikr functions are withing quikr.function name
fix quikr_train to work with updated quikr module
moving some stuff
adding matlab code
move python stuff to python directory
removed documented matlab, add bare makefile
removed  multifasta's py extension, modified the --help argument output for quikr_train
initial commit of some documentation
updated makefile to install nbc properly and python properly.