I'll just explain the new pieces of code:$h{$F[0]}{$F[3]}++ - This will create "hash of hashes", with first key being 1st field in your file, and second key being field number four. This technique is described in "Intermediate Perl" book. So after running this code over your sample file, the %h hash structure looks like this:

Code:

 %h = {
          'scplasm1' => {
                          '6153' => 1
                        },
          'chr01' => {
                       '12745' => 3
                     },
          'chrm' => {
                      '86086' => 2,
                      '98064' => 1
                    }
        };

As you can see, for each $F[0] field, all the $F[3] fields are present as keys of underlying hash. Values stored in those inner hashes are number occurrences for $F[3] field. This code would also work without storing this information, using: $h{$F[0]}{$F[3]}=1, then hash will look like this:

Code:

%h = {
          'scplasm1' => {
                          '6153' => 1
                        },
          'chr01' => {
                       '12745' => 1
                     },
          'chrm' => {
                      '86086' => 1,
                      '98064' => 1
                    }
        };

Now all we have to do is print the number of keys present in each inner hash (blue) for each main hash key - $F[0] field (red). To do this we iterate over $F[0] values (red) using for $i (keys %h){Then we assign inner hash keys (blue) to @x array - @x=keys %{$h{$i}};. So during each for each $i value, @x will look like this:

Code:

$i = scplasm1
@x = [
          '6153'
        ];

$i = chr01
@x = [
          '12745'
        ];

$i = chrm
@x = [
          '86086',
          '98064'
        ];

Now all we have to do is print $i and respective number of elements of @x array: print "$i\t" . ($#x+1) . "\n"