Snapshot of some things I might want to look back at.

Nothing really great, but especially in the commented blocks there's
some stuff that I might want to go back to doing.
Functional. Stash before complete refactor

Well, I did just discover that it seems that nhmmscan is less sensitive
than hmmscan
Refactor into separate classes
actually make partitions

write out files with partition info -- i.e. a column with seq id and a
column with group id -- suitable to be read by compare_clustering.py

Well, it kinda sucks at the moment, but it gets adj_mi around 0.3

Time to iterate!