ENH: method to compute a taxonomy based index
TST: tests for index computation
TST: added script usage test
ENH: allow for specifying an output column name
ENH: support for an arbitrary key
Addressing @ElDeveloper's comments
Addressing more of @ElDeveloper's comments
Fixed spacing
ENH: can dump to a mapping file, thanks @ElDeveloper
DOC: changelog mention
DOC: mapping file mention in output
DOC/ENH: typo and closing a file better now
Merge branch 'master' of github.com:qiime/qiime into dysbiosis_index

Conflicts:
	ChangeLog.md
Fixes #1025, spaces in id-to-taxonomy file break assignment with Mothur.
Fixed error when output_fp was not None.
Added test to cover output to file, fixed bug in formatting lineages.
Address comments from code review.
Address second round of code review comments: properly re-format taxa with multiple consecutive spaces, add try/finally block to close re-formatted taxa file while running app, removed extra temp file in test.
BUG: zerodiv error when numerator is 0... weird
Merge pull request #1725 from kylebittinger/mothur-spaces

Fixes #1025, spaces in id-to-taxonomy file break assignment with Mothur.