Hello mate,
please describe in plain steps
how exactly works the algorithm for receiving the desired output.

update
check if this what you want

use Inline::Files;

push @b, [split ' '] for <FILEB>;

while (@a = split ' ', <FILEA>){
    --$_ for @a;
    print "@{$b[0]}[@a]\n";
    for $i (1.. $#b) {
        undef @h{@{$b[$i]}[@a]};
        $s++ if scalar keys %h == 1;
        undef %h;

    }
    print "$s\n" if $s;
    undef $s;
}

__FILEA__
1 2 3 4
1 2 3 5
1 2 4 5
1 3 4 5
2 3 4 5

__FILEB__
A    B    C    D    E    
0    0    0    +    0    
+    0    +    +    +    
0    +    +    +    +    
0    0    +    +    0    
+    +    +    +    +    
0    +    +    +    +    
+    0    +    +    0
[download]

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