code: def phmmer(query, db, type, out, threads = '4', evalue = '0.01'):
      
      if os.path.exists(out) is False:
          print('# ... running phmmer with %s as query and %s as database' % (query, db))
          os.system('phmmer -o %s.ph1 --tblout %s.ph2 --acc --noali --notextw -E %s --cpu %s %s %s' % (out, out, evalue, threads, query, db))
      else:
          print('# ... phmmer output found for %s as query and %s as database' % (query, db))
      phmmer2blast('%s.ph2' % out, out)
docs: run phmmer