my $locus;

while (<$in>) {
    if ( /LOCUS\s+(\w+)/ ) {
        $locus = $1;
    }
    elsif ( /\^\^/ ) {
        if ( $locus ) {
            s/\^\^/>$locus\n^^\n/g;
        }
        else {
            warn "Found ^^ without a preceding LOCUS value\n";
        }
    }
    print $out $_;
}

##</code><code>##

        ( $locus ) = ( /LOCUS\s+(\w+)/ );