I have here a little thing called swap_row_col.pl. It's very old (my filesystem says I haven't touched it in more than 4 years) so I just refactored it now. Once swapped in this way, the data can be List::Util::shuffle'd and swap_row_col'ed again. This is tested:

use warnings;
use strict;
use List::Util qw/shuffle/;

sub swap_row_col {
    my @swapped;

    foreach (@_) {
        chomp;  ## just in case
        my @elems = split /;/;
        for (my $i = 0; $i < @elems; $i++) {
            exists $swapped[$i] and $swapped[$i] .= ';';
            $swapped[$i] .= $elems[$i];
        }
    }
    return @swapped;
}

my @vshuffled = swap_row_col shuffle swap_row_col <DATA>;

__DATA__
one;two;three;four
foo;bar;baz;qux
yellow;red;blue;green
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The output from Data::Dumper is something like this:

$VAR1 = [
          'one;three;four;two',
          'foo;baz;qux;bar',
          'yellow;blue;green;red'
        ];
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