You're putting a while loop to read a file inside of a for loop that reads another file. However, you've not told perl to restart the file at the beginning just before your while loop. So the first time through your for loop, you read one line of the first file and the entire second file. At the next iteration of your for loop, you read the second line of the first file, and *nothing* from the second file because you've already read it all.

The simplest (and least efficient) fix would be to close the second file after your while loop, and open it just before the while loop.

A better fix would be to read the second file into an array first, and then in your for loop you can simply loop over the array containing the second file.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

But its certainly not a good idea to read <AB> again and again in a loop processing the lines in <BC> (i.e. @file ).

So put the <AB> stuff into an initialization part populating @coll just once, that is before looping.

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]

Hello! sorry for late reply.

Algorithm include following steps:

1. accessing each line of file 2

2.and parsing these elements to while loop(so on accessing the respective columns)

3.comparing those columns in for loop

No, I meant
how does every line like 1 2 3 4
relate to the file1 ?
We take only 1 2 3 4 columns from file1?
A B C D? what is the logic we're trying to achieve at the end?
To summarize the column's pluses and zeroes in different arrays?
Maybe it is an XY problem we're facing here.
At this point I got this:
we take the first line 1 2 3 4, decrement every element,
then in a loop we push 4 elements into different four arrays according to these values.
At the end we're getting four arrays that look like this:
A0+000+0A0+000+0A0+000+0A0+000+0A0+000+0.
So what's the end goal?

#!/usr/bin/perl
use strict;
use warnings;
use Algorithm::Combinatorics 'subsets';

my @headers = split ' ', scalar <DATA>;
my @data = map [split], <DATA>;

my @subsets;
for my $k (3, 4) {
    push @subsets, subsets([0 .. $#headers], $k);
}

for my $indices (@subsets) {
    my $count = 0;
    for my $aref (@data) {
        ++$count unless grep $_ eq '0', @$aref[ @$indices ];
    }
    print "@headers[ @$indices ]\t$count\n";    
}

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

A B C   1
A B D   1
A B E   1
A C D   3
A C E   2
A D E   2
B C D   3
B C E   3
B D E   3
C D E   4
A B C D 1
A B C E 1
A B D E 1
A C D E 2
B C D E 3
[download]

Thank you very much. Your code is working perfectly fine on my dataset.