Others have replied regarding your question, so I leave that. But I do want to suggest that the variable $line should be removed here. This is mostly a style question, but imho the code gets a lot nicer if $_ is used instead of another variable. The infamous $line is over-used, if you ask me.

    foreach (@rows) {
        s/\t/\x09/ig;
        s/\n/\x0A/ig;
        s/\r/\x0D/ig;
        s/"/'/ig;
        print FILE qq{"$_",}; # Other delimiters too.
        $cell++;
    }
[download]

Other issues with this code are left aside.

ihb