open SEQ,  '<', $ARGV[0] or die $!; #plain
open MASK, '<', $ARGV[1] or die $!; #hardmask

while ( my $seq = <SEQ> ) {    ## Read a sequence 
    my $mask = <MASK>;         ## And the corresponding mask

    if ( $mask =~ /^>/ ) {    
        print "$seq";
    }
    else {
        $mask =~ tr[N][ ];         ## Ns => spaces
        print $seq | $mask;        ## bitwise-OR them and print the result;
        
    }
    
}
close SEQ;
close MASK;