Yes, I glossed over the output management part, thinking the OP probably had a handle on that already (unfortunate pun duly noted).

As often as not for things like this, I just make the script print to STDOUT and put the file handling stuff on the command line -- why right write more lines of perl code to do stuff that the shell can do for me with an angle bracket? 

text-altering-script.perl  input.file > output.file

# optional step:
mv output.file input.file

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In reply to Re^3: Searching and replacing text by graff
in thread Searching and replacing text by Anonymous Monk

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