use strict;
use warnings;

my @rows;
while ( <DATA> ) { 
 chomp;
 #split row and put in anon array pushed into @rows
 push @rows, [ split /\|/ ]; 
}

#sort @rows (an Array of Arrays) by column;
#@rows looks something like: (ARRAY(0x...),ARRAY(0x...),..)
#where ARRAY(0x...) is just a reference to another array.
my @sorted = sort { $a->[2] <=> $b->[2] } @rows;

#since @sorted is now an array of Arrays sorted 
#we need to dereference what's in it to print it.

foreach my $array_reference ( @sorted ){
  #lets join the array pointed to in the array reference 
  # with a "|"
  # @ dereferences the array
  #and print
  print join("|",@$array_reference),$/;
}

__DATA__
My|Text|5|ACGT 
My|Text|2|ACGT 
My|Text|4|ACGT 
My|Text|3|ACGT 
My|Text|1|ACGT