Refactored rtax code to be less repetitive and use _directory_check method
Refactored rtax code to be less repetitive and use _directory_check method

caporaso-lab/short-read-tax-assignment,gregcaporaso/short-read-tax-assignment,nbokulich/short-read-tax-assignment,BenKaehler/short-read-tax-assignment,caporaso-lab/tax-credit