Major commit to add script usage examples and other changes

Addressed minor errors in a host of places and added documentation. Also finalized paired t test functionality
Deleted otu_category_significance.py
Finished run_ocs_test unit tests, mod bon_corr to return list
Merge branch 'ocs_collab' of https://github.com/wdwvt1/qiime into ocs_collab
more tests...
added unit tests
updated output formatter to work with taxonomy strings, updated unit tests
small doc change
modified sort_by_pval and unit tests
Move conversion code to stand-alone lib
corr unit tests added
Modified documentation and small changes

Small changes to code for fdr calculations and verbosity options.
minor additions
Merge branch 'ocs_collab' of https://github.com/wdwvt1/qiime into ocs_collab

Conflicts:
	qiime/ocs.py
	tests/test_ocs.py
Fix import statement
Fix code guidelines
Correct Sample ids to be MIENS compliant
Multiple modifications

Renamed the script ocs.py to test_group_significance.py.
Renamed the library ocs.py to otu_significance.py (both group tests and correlation tests will use it)
Placed relavent functions in qiime.utils.
Placed tests for those functions in tests/test_utils.py
Rewrote Mann-Whitney U test to make it faster/cleaner and to prevent behavior when using mw_boot where it would stochastically error. The reason it stochastically errored was because if it would randomly choose two samples which were all the same, then the ranks would all be equal, and the denominator of the modified t statistic would drop to zero. It now returns nan for a pvalue in this case.
Added a large number of tests to pycogent_backports/test.py.
Rewrote the subsampling routine for the mc_t_two_sample test to avoid stochastic errors that were caused by differently ordered vectors.
Modified commit message. Major changes to tests.

Modified default FDR procedure used by several scripts to be Benjamini Hochberg's step down procedure. Moved BH correction and Bonferroni correction to pycogent_backports/tests.py.
Added tests of functions added to qiime/utils.py.
Added option for number of permutations to scripts/test_group_significance.py for the bootstrapping methods.
Altered the way the mc_t_two_sample test does permutations to ensure that that if permuted columns are passed to it, the answer remains the same (as it should mathematically).

   (use "git add <file>..." to update what will be committed)
Updated and added tests.