code: def run_cmsearch(fastas, threads, cm):
      
      out = []
      for fasta in fastas:
          cmsearch = '%s.23S.cmsearch' % (fasta.name.rsplit('.', 1)[0])
          if os.path.exists(cmsearch) is False:
              p = Popen('\
                      cmsearch --cpu %s --hmmonly --acc --noali -T -1 --tblout %s %s %s >> cmsearch.log' \
                      % (threads, cmsearch, cm, fasta.name), shell = True)
              p.communicate()
          else:
              print('# cmsearch output found: %s' % (cmsearch), file=sys.stderr)
          out.append(open(cmsearch))
      return out
docs: run cmsearch: comapre 23S sequences to ssu-align's CM