Remove unused imports
Remove cast to Dict2D in mapping_file_to_dict
Remove useless import
Remove useless import
Changing cogent.core.alignment.eps by np.finfo(float).eps
Remove Dict2D in make_compatible_distance_matrices

We are now using pure python to filter out the data from the distance
matrices.
Merge branch 'master' of git://github.com/qiime/qiime into torpedo-dict2d

Conflicts:
	tests/test_otu_significance.py
Merge branch 'torpedo-dict2d' of github.com:ElDeveloper/qiime into torpedo-dict2d
Remove unused import
Use numpy's advanced indexing

Thanks @ElBrogrammer!
Merge branch 'master' of git://github.com/qiime/qiime into torpedo-dict2d

Conflicts:
	qiime/util.py
Merge branch 'master' of git://github.com/qiime/qiime into torpedo-dict2d

Conflicts:
	tests/test_otu_significance.py
Fix special case of an empty intersection

Thanks @ElBrogrammer!!
Make the construction of a 2D dict cleaner

Thanks for the pointer @wasade!
Merge branch 'master' of git://github.com/qiime/qiime into torpedo-dict2d
Revert "Make the construction of a 2D dict cleaner"

This reverts commit 8427c1cdd8d06c6c924f5573781fdf70c93da123.
Adding close(-) statements
Merge branch 'master' of https://github.com/qiime/qiime into fixing_mkstemp_close_fd
Merge branch 'master' of https://github.com/qiime/qiime into fixing_mkstemp_close_fd
Fixing merge conflicts