Add sortmerna to assign_taxonomy.py

Partially resolves https://github.com/gregcaporaso/short-read-tax-assignment/issues/68.

Most of the functions follow those in https://github.com/ekopylova/short-read-tax-assignment, with modifications relating to Null alignment strings now output by sortmerna.

Change: 

'Option --similarity must be between (0,1].'

to:

'--similarity must be between (0,1].'

(and make the same change for the error messages below).