Simplify compare_biom.py script
Fix print_picrust_config.py

Fix #112
Fix categorize_by_function.py

Fix #110
Change allows more flexiblity in the type of metadata that can be used to collapse counts by.
Previouly only lists of lists where allowed and now list of strings are allowed.
Code provided by @zanevled and I just implemented and tested.

Allow more flexibility in the types of
Add script level test data for categorize_by_function.py
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.
Fix COG_Category metadata

COG_Category is now formatted as lists of lists,
so categorize_by_function.py will work properly.

Names of COG categories have been added in addition to just the
single letter COG category code.

Also, the first (highest level) is now one of the 4 groups that the
COG category belong to, so they can be collapsed at both level 1 and 2.

Fix #120
Merge pull request #113 from mlangill/issue112

Fix print_picrust_config.py
Merge pull request #103 from mlangill/cleanup_compare_biom_script

Merging.  However, we may separately want to update the documentation to be more clear about  accuracy criteria.  E.g. that binary presence/absence scores are used unless the data are relative.
Merge pull request #119 from mlangill/issue118

Adds more user-friendly option for specificying function type
Merge pull request #116 from mlangill/issue110

Fix and add testing for categorize_by_function.py
Merge pull request #121 from mlangill/issue120

Fix COG_Category metadata