Now drops NAs from analysis

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3210 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Now drops NAs from analysis, works with no NAs

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3211 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated cytoscape_usage to direct to tutorials/making_cytoscape_network

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3212 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Updated mothur module in PyCogent backports


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3213 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
subsample prior to transform in get_rare_data

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3214 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
make_distance_boxplots.py and make_distance_comparison_plots.py can now perform Student's two-sample t-tests to determine whether a pair of boxplots/distributions are significantly different (using both parametric and nonparametric Monte Carlo-based tests of significance). These changes include three new options to the two scripts (--tail_type, --num_permutations, and --suppress_significance_tests), as well as a new function all_pairs_t_test in qiime.stats. The accompanying tutorial has also been updated to cover the new statistical tests.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3215 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added warning about not using asymmetric distance matrices to several areas of code that assume symmetric matrices.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3216 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Now allows unquoted single quotations

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3217 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added more documentation to distance plotting scripts and tutorial that instruct users what to do if their plots are messed up. Synced with pycogent.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3218 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Now produces mislabeling.txt and cv_probabilities.txt that look like mapping files, and with binary mislabeling classification columns for use with filter_samples_from_otu_table

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3219 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added check for asymmetry and non-hollowness to appropriate areas in the code.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3220 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modfied stochastic test to be a bit more lenient.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3221 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
removed imports from qiime in preparation for port to pycogent

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3222 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Sync'd distribution_plots.py with PyCogent to get tight_layout() functionality.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3223 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Remove qiime_config import from rtax to allow backport to pycogent

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3224 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
rtax should use get_qiime_temp_dir

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3225 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Removed qiime dependency from test_rtax.py.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3226 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated the writing of files when passing -w....this was broken on may 7th



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3227 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Synced pycogent backports muscle app controller with pycogent.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3228 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
make_phylogeny.py now uses pycogent_backports.muscle_v38.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3229 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a