Added support for gzipped SFF files

Modified qiime.process_sff to use qiime_open in 'rb' mode (default 'U' mode
does not work), added a gzipped SFF file to test_support_files, and modified
test_process_sff.py to perform all the tests on the gzipped file in addition
to the non-gzipped file.
Moified doc string for qiime_open

Doc string now warns to be sure to open binary files in a binary mode;
default mode of 'U' opens in text mode.
Merge pull request #427 from adamrp/process_sff

Added support for gzipped SFF files
Modified pick_otus.py BLAST picking method

Now uses path.abspath when passing reference sequences path.
Modified pick_otus.py to use abspath

No longer fails when using relative paths.
Modified pick_otus and test_pick_otus

pick_otus now uses abspaths (including for log files) for refseqs file paths,
and the test script now expects those absolute paths to be logged.
Added utility methods to MetadataMap class to check for numeric categories, unique categories, and single-value (non-varying) categories. Modified CategoryStats class to allow restrictions to be placed on the type of categories that a statistical method will accept (e.g. the category must be numeric, or it must specify more than one group of samples, etc.).
Fixed issue 432
Merge pull request #433 from danknights/master

Fix Issue 432
Significant refactor of underlying code to be better tested and maintained easier (new qiime/compare_categories.py and tests/test_compare_categories.py modules); added better error checking and handling for the types of categories that are accepted by the statistical methods (e.g. checking that categories are numeric if they need to be, making sure categories do not contain all unique values, or a single value); fixed output format for BEST method to be easier to read and consistent with the other methods; qiime.util.MetadataMap class has a few new utility methods to suppport some of these changes.
Fixed several scripts that were not using %prog in their usage examples. This should remove the warnings that were seen when running the script usage example tests in qiime_test_data. This fixes issue 64 in the qiime_test_data repo.
Added, base work for add_alpha_to_mapping_file
Updated test data, all tests are passing
clarified shotgun_analysis.rst docs, and fixed typos
Fixed issue where script was still looking in pycogent_backports for raxml, pplacer, etc.. These app controllers are now in pycogent.
Merge pull request #439 from justin212k/shotgun_doc

clarified shotgun_analysis.rst docs, and fixed typos
Merge pull request #428 from adamrp/pick_otus

Pick otus
Merge pull request #440 from jrrideout/insert_seqs_into_tree

Fix for insert_seqs_into_tree.py: location of app controllers
Merge pull request #437 from jrrideout/qiime_test_data_issue_64

Fixed several scripts that were not using %prog in their usage examples....
Merge pull request #434 from jrrideout/issues_423_424

Fixes for issues #423 and #424.