length probably isn't doing what you think it does. Try: for($k = 0; $k < @PAR1; $k++).

Or, even better:

for my @PAR1_info (@PAR1) {
     
        $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/$cove
+rage_sum));
}
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Edit: As AnomalousMonk pointed out, the above code doesn't compile. That's what I get for neither thinking nor testing. What I thought I was thinking was more like the following, which does compile (after a bit of testing, fixing bugs and making presumptive changes):

    $pi_sum = 0;
    $L_sum = 0;
    $differences_sum = 0;
    $coverage_sum = 0;
    for my $PAR1 (@PAR1) {
            
        my @PAR1_info = split(/\t/, $PAR1);

        $pi = $PAR1_info[0];
        $pi_sum = $pi_sum + $pi;
    
        $L = $PAR1_info[1];
        $L_sum = $L_sum + $L;
    
        $differences = $PAR1_info[2];
        $differences_sum = $differences_sum + $differences; 
    
        $coverage = $PAR1_info[3];
        $coverage_sum = $coverage_sum + $coverage;
    

           my $PAR1_diversity = (($pi_sum/$L_sum)/($differences_sum/$c
+overage_sum));
    }
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Which could be reduced to:

    $pi_sum = 0;
    $L_sum = 0;
    $differences_sum = 0;
    $coverage_sum = 0;
    for my $PAR1 (@PAR1) {
            
        my ($pi, $L, $differences, $coverage) = split(/\t/, $PAR1);

        $pi_sum = $pi_sum + $pi;
    
        $L_sum = $L_sum + $L;
    
        $differences_sum = $differences_sum + $differences; 
    
        $coverage_sum = $coverage_sum + $coverage;
    

           my $PAR1_diversity = (($pi_sum/$L_sum)/($differences_sum/$c
+overage_sum));
    }
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And, prior to this, chomping the input is probably appropriate:

my @X_info = <CHR_X_INPUT>;
chomp(@X_info);
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