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if ($ARGV[0] eq "new") {
 @hex = system("/home/testuser01/new.php $ARGV[0] > $path$r_file");
...
#Comment 2
*333 23 ss id: 002 aaa bbb ccc
*22 233333333 34432 233 44

#Comment
*333 23 ss id: 002 aaa bbb ccc
...
#Comment 2
*ss id addr id: 099 bbb ccc aaa
*22 233333333 34432 233 44

unlink("$path$rfile");
open(FILE, "/home/testuser01/") || die "Count not open old Gen_file";
...
                              } @matching_lines;
@lines[@matching_indices] = @sorted_matching_lines;
print @lines;