while ( my $line = <FILE> ) {
    foreach ( 0 .. $#first_half ) {
        $line =~ s/$first_half[$_]/$second_half[$_]/;
    }
}
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Might be a better design philosophy to set up the LHS as keys and RHS as values to a hash, and just iterate over the keys. But that's a matter of choice; either way works. Also, remember to use \Q \E if necessary, or pass RE objects using qr//.