Edits have been made to A Question with Nesting Arrays and I can explain more clearly now. I did indeed mean to restructure my input data by sampling with replacement, not shuffling. Each element of the input array is a string of characters, comprised itself of 4 tab delimited elements (shown below)

 
A1   B1   C1   D1
A2   B2   C2   D2
A3   B3   C3   D3
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After restructuring my data I further subdivide the new array  @tmp with the splice function. With the last for loop and looping variable k I wish to assign each of the four elements in a string to 4 separate variables. The difficulties I am encountering: the code below assigns the length of the string, 4, to each of my variables and the for loop does not loop. For example I wish the variable pi to equal A1 but it is assigned the value 4. I don't understand why the split function isn't working or why the last for loop doesn't loop/increase k.

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 in
+put";
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 arr
+ay    
        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_su
+m/$coverage_sum));

    }

}
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