Just a few pointers that will help you find the problem. The following will help you find errors in your code.

#!/usr/local/bin/perl -w

use strict;
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When opening files it is a good thing to check to see if they actually opened or not.

open(FH, "<file.txt") or die "Could not open file.txt: $!\n";
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The webserver will most likely be running under a different user then yourself and will have to have access to the files your are opening and modifing.

Hope this helps.

-bn