Add preprocess_mapping_file and tests

This function serves as a controller for all the pre-processing that
might be needed prior to formatting the mapping file data into java
script.
Remove process_mapping_file from emperor.util

process_mapping_file has now been substituted by preprocess_mapping_file
this function will take the responsability of a controller function,
managing tasks related with curating the metadata for other functions in
the script scripts/make_emperor.py
Add --color_by option to script interface

You can now select what are the metadata categories of interest you want
the PCoA plot to be colored by.

Some clean-up was done in the script interface.

This should fix #4
Merge pull request #20 from ElDeveloper/issue_4

Fix issue #4 - Add --colory_by option