def _cmd_miraligner(fn, out_file, species, hairpin, out):
tool = _get_miraligner()<EOL>path_db = op.dirname(op.abspath(hairpin))<EOL>cmd = "<STR_LIT>"<EOL>if not file_exists(out_file):<EOL><INDENT>logger.info("<STR_LIT>" % fn)<EOL>do.run(cmd.format(**locals()), "<STR_LIT>" % fn)<EOL>shutil.move(out_file + "<STR_LIT>", out_file)<EOL><DEDENT>return out_file<EOL>
Run miraligner for miRNA annotation