Once you take away what doesn't matter, and boil it down to a simplified test script, you're left with this:

@f = <DATA>;
foreach $line (@f) {
  @AB = split("\t", $line);
  @AA = sort { $a->[1] <=> $b->[1] } @AB;
  foreach $temp (@AA) {
    print "@$temp\t", "\n";
  }
}
__DATA__
AA 34
AB 22
AC 12
[download]

...which indeed has the appearance of not running.

If you modify the script to be strict compliant, you have this:

use strict;
use warnings;
use diagnostics;

my @f = <DATA>;
foreach my $line (@f) {
  my @AB = split("\t", $line);
  my @AA = sort { $a->[1] <=> $b->[1] } @AB;
  foreach my $temp (@AA) {
    print "@$temp\t", "\n";
  }
}

__DATA__
AA 34
AB 22
AC 12
[download]

And when you run that, you get:

Can't use string ("AA 34
") as an ARRAY ref while "strict refs" in use at mytest.pl line 12, <D
+ATA> line 3 (#1)
    (F) Only hard references are allowed by "strict refs".  Symbolic
    references are disallowed.  See perlref.
    
Uncaught exception from user code:
    Can't use string ("AA 34
") as an ARRAY ref while "strict refs" in use at mytest.pl line 12, <D
+ATA> line 3.
 at mytest.pl line 12, <DATA> line 3.
[download]

Now why might we be getting a "strict refs" violation? Probably because inside your sort routine, you're dereferencing elements of an array that don't hold a reference.

Once you solve that, the next problem will be to sort rows based on columns, rather than columns based on columns.