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