First, try simplifying your code. Troubleshooting overly-verbose code larded with unnecessary variables and routines is difficult.
perl -wpe's/my_pattern/my_replacement/g' in_file > out_file
This will do what you're looking for (the '-p' option creates a printing loop around the specified in_file.) After that, if you want to expand it, you can - one step at a time and checking the output after every change. That should be a pretty good way to learn about these functions and their command line equivalents (see perlrun for more info on the various options to perl.)
--
"Language shapes the way we think, and determines what we can think about."
-- B. L. Whorf
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