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print $file $_ if s/$LeftSide/$RightSide/eegi;

print $_ if s/$LeftSide/eval $RightSide/egi;

# main.pl

...
__DATA__
(123),(456),(789)
(abc),(def),(ghi)

# prepare_run.pl

...
close($run);

system("run.pl"); #or whatever the the equivalent of your OS.

# run.pl, will be created after running "prepare_run.pl" while using "
+main.pl" as a template.

...
__DATA__
(123),(456),(789)
(abc),(def),(ghi)

(123)
(456)
...
(abc)
(def)
(ghi)