use strict;

my ($handle, @header, @file1, @file2, $row, $col, @output);

### Load header data
open ($handle, 'header.txt')
    || die "Can't load header file.\n";

while (<$handle>) {
    @_ = split /,/, $_;
    $_ = pop @_; chomp;

    push @header, $_;
}
close ($handle);

### Load file 1 as array of arrays
open ($handle, 'file1.txt')
    || die "Can't load data file 1.\n";

while (<$handle>) {
    push @file1, [split /,/, $_];
}
close ($handle);

### Load file 2
open ($handle, 'file2.txt')
    || die "Can't load data file 2.\n";

while (<$handle>) {
    push @file2, [split /,/, $_];
}
close ($handle);

### Output header line
print join "\t", @header; print "\n";

### For each line, output x for fields with a difference
for ($row = 0; $row <= $#file1; $row++) {
    @output = ();
    for ($col = 0; $col <= $#header; $col++) {
        push @output, $file1[$row][$col] ne $file2[$row][$col] ?
            'x' : '';
    }
    print join "\t", @output; print "\n";
}