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
Fix typo in script data directory start_parallel_jobs_sge
Add system_call function

system_call() will be used in new all_tests.py script and
is based off of qiime_system_cal()
Add script level testing

In addition to module testing, all_tests.py will run each script and
check for proper completion. The script level testing is only done if
QIIME is installed (otherwise it is skipped without errors) since
it calls functionality from that package.

Fix #78.
Fix reference before assignment error when QIIME is not installed.
Update all_tests.py

Add myself to credits list and indicate that code is based off of QIIME's all_test.py code (instead of using previous biom-format code).
Update util.py

Add note indicating that system_call() came from QIIME's qiime_system_call()
Merge pull request #122 from mlangill/issue78

Add script level testing to all_tests.py
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
Improved caching and lookups
removed extra comments and whitespace, weighted avg passed node not name