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));
}
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));
}
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));
}
And, prior to this, chomping the input is probably appropriate:
my @X_info = <CHR_X_INPUT>;
chomp(@X_info);