SortMeRNA updates and latest tables

Bit of a big PR...
I guess that if we don't forsee these functions disappearing in the
future, then it's fine to leave as is. Up to you.

On (Dec-03-14| 8:23), Daniel McDonald wrote:
> > @@ -67,7 +68,8 @@ def load_category_files(category_files):
> >  
> >      for (category, category_file) in category_files.iteritems():
> >          if isfile(category_file):
> > -            cat_table = parse_biom_table(open(category_file, 'U'))
> > +            with biom_open(category_file, 'U') as fp:
> 
> Probably... but this works and is functionally equiv. Can change if you'd like tho
> 
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> https://github.com/biocore/American-Gut/pull/116/files#r21242798