A1   B1   C1   D1
A2   B2   C2   D2
A3   B3   C3   D3


##</code><code>##


my $runs = 1;           # for testing code
#my $runs = 1000;	   # 1_000 - the num of times we repeat 
#my $runs = 100000;     # 10 _000 - the num of times we repeat 
#my $runs = 1000000;    # 100_000 - the num of times we repeat

# Program vars
my $i;					# a looping variable
my $j;					# another looping variable
my $k;					# another looping var
my $range = 1552; 	    # total number of array elements
my @tmp;			      # empty array to push data into

#Looping Variables
my $pi;
my $pi_sum;
my $L;
my $L_sum;
my $differences;
my $differences_sum;
my $coverage;
my $coverage_sum;

;
;

my $chr_X_input = "bootstrap_data.txt";
open (CHR_X_INPUT, "<$chr_X_input") or die "can't open chromosome X input";
my @X_info = <CHR_X_INPUT>;

# Outer loop: Repeat "$runs" times 
for ($j = 0; $j < $runs; $j++) {

	for ($i = 0; $i < $range ; $i++) {
	
		# choose a randomly selected string of 4 elements from our array	
		push (@tmp, $X_info[int(rand($range))]);
		
	}

	my @PAR1 = splice(@tmp, 0, 26,); 
		
	for ($k = 0; $k < length(@PAR1) + 1 ; $k++) {
			
	    my @PAR1_info = $PAR1[$k];
		
	    $pi = split('\t', $PAR1_info[0]);
	    $pi_sum = $pi_sum + $pi;
	
	    $L = split('\t', $PAR1_info[1]);
	    $L_sum = $L_sum + $L;
	
	    $differences = split('\t', $PAR1_info[2]);
	    $differences_sum = $differences_sum + $differences; 
	
	    $coverage = split('\t', $PAR1_info[3]);
	    $coverage_sum = $coverage_sum + $coverage;
	

       	    my $PAR1_diversity = (($pi_sum/$L_sum)/($differences_sum/$coverage_sum));

	}

}