code: def _cmd_miraligner(fn, out_file, species, hairpin, out):
      
      tool = _get_miraligner()
      path_db = op.dirname(op.abspath(hairpin))
      cmd = "{tool} -freq -i {fn} -o {out_file} -s {species} -db {path_db} -sub 1 -trim 3 -add 3"
      if not file_exists(out_file):
          logger.info("Running miraligner with %s" % fn)
          do.run(cmd.format(**locals()), "miraligner with %s" % fn)
          shutil.move(out_file + ".mirna", out_file)
      return out_file
docs: Run miraligner for miRNA annotation