Add unit testing plan outline
Updated call script and testing plan
Moved all I/O in test_cospeciation.py into main()

Started to pare down test_cospeciation.py into testable fragments.
Began by moving all the file I/O into the Main but preserving all
other structure. Tested and gave same output.
some streamlining of the main code
Added the ToDos folder and unit test script.
cogent_dist_to_qiime_dist and associated unit test added to test_cospeciation.py and test_test_cospeciation.py, respectively
modified cogent_dist_to_qiime_dist to output ordered list; improved its associated unit test
Restructuring of make_dists_and_tree and addition of accessory methods

I rewrote make_dists_and_tree so that it takes a file path and list of host names and checks if the file at the given path is a distance matrix, sequence alignment, or tree and processes them accordingly, generating a distance matrix and/or tree if necessary. It then trims both of these according to the list of sample names and returns them to main(). Note: we discussed integrating the contents of this method into main in a future revision, as its seperation serves no significant purpose.
Minor reconfiguration of make_dists_and_tree and helper methods

Moved file-reading for host information file (matrix or tree or alignment) out of individual methods and into make_dists_and_tree. The associated process methods now require a string with contents of the file, not the file path.
Fixed syntax error on line 1027 and I don't know how to undo the last commit so I'm doing another one.
Host matrix/alignment/tree processing functions now work

The isTree, isAlignment, isMatrix, processTree, processMatrix, and processAlignment methods now work when passed the contents of the file as a string. The cogent_dist_to_qiime_dist function was also updated to convert sparse matrices into padded matrices.
added cogent_dist_to_qiime_dist
incorporated Aarons version of cogent_dist_to_qiime_dist
Added Aarons hommola_cospeciation_test
Added Nates tree and dist import functionality.
revamped recursive_hommola to use updated dm format
Added Nates sparse dm fix to cogent_dist_to_qiime_dist
Added option to do Hommola test non-recursively
Fixed problem of retaining empty cOTUs in matrix
Aaron: removed pOTU integer sorting from summarize_results; updated test_cospeciation to only test cOTUs found in the OTU table (rather than testing all subclustered cOTUs).