Map is your friend!!!!!! jeffa wrote a nice little tutorial about it here

A quick example that "should" help on your comma to pipe switch issue.

open (FILE, "foo.txt");
    my @lines = map { s/,/|/g; $_; } <FILE>;
close FILE;
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Mind you this is just a snippet taken and modified from the tutorial. You might need a little more "tunning" for your needs.