use strict;
use warnings;
use List::Util 'shuffle'; # Idea from http://www.perlmonks.org/?node_id=199901

my $input = shift @ARGV;
open(IN, '<', $input) or die "Can't read multifasta input genomic DNA file $input : $!\n";

my $window = 1000000; # hard coded for shuffle window to be 1MB i.e 10^6

my (@IDsSeqs,$seq_id, $seq, @output);

while (<IN>) {
    chomp;
    push @IDsSeqs, $_;
    }

my $index = 0;

while ($index <= $#IDsSeqs)			{

	$seq_id = $IDsSeqs[$index];
	$seq = $IDsSeqs[$index+1];

    my $final_seq;

		for (my $i = 1; $i <= length $seq; $i=$i+$window ) {
		    my $s = substr ($seq, $i - 1, $window);
		    my @temp_seq_array = split //, $s;
			my $rep = 1;
			
			while($rep <=10)		{
		    @temp_seq_array = shuffle @temp_seq_array; # using the List::Util module AND Shuffles EACH windown 10 times!!!
			$rep++;
			 }
		   my $rand_shuffled_seq = join ('', @temp_seq_array,);
		    $final_seq = $final_seq.$rand_shuffled_seq; # concatenates the shuffled DNA seq to the 3' end of the previous 1MB fragment
	}
    push @output, $seq_id, "\n",$final_seq,"\n";

$index = $index + 2; # process every alternate line with ID (and its corresponding sequence in next line)
}

my $destination = $input."_1MBWindow_ListUtilshuffle.fasta";
open(OUT, '>', $destination) or die "Can't write to file $destination: $!\n";
print OUT @output;
close OUT;