Something like this can work:

#!/bin/perl
use warnings;
use strict;

my @array;
my $rows = 0;
my $columns = 0;
while(<DATA>) {
    chomp;
    $rows = length($_);
    for ( my $j = 0; $j < $rows; $j++ ) {
        $array[$columns][$j] = substr($_, $j, 1);
    }
    $columns++;
}
for ( my $m = 0; $m < $rows; $m++ ) {
    for ( my $k = 0; $k < $columns ; $k++ ) {
        print $array[$k][$m];
    }
    print "\n";
}

__DATA__
12345
12345
12345
12345
12345
12345
12345
12345
12345
12345
12345
12345
12345
[download]

With the output:

C:\Code>perl swap.pl
1111111111111
2222222222222
3333333333333
4444444444444
5555555555555
[download]

But it has to be noted, I think this topic has been touched on at least twice in the last month.