More details. The infile is actually a list of lists having each sublist a header and two numbers separated by tab. The first loop reads the infile and creates these little arrays associated with each sublist that I called $currentPop. The second loop goes through each array of @ total, splices one randomly chosen element and pushes into @{$RandHapl{$_}}. I then use this following code for printing a new file.

foreach $Population (@total) {
    print "Population $Population\n";
    print OUT "Population $Population\n";
    print "$sampleSize{$Population}\n";

    for($i = 0; $i <  $sampleSize{$Population}/2; $i++) {
        @pair = splice @{$RandHapl{$Population}}, 0, 2;
        #print "[@pair]\n";
        print "$pair[0][0]\t$pair[1][0]\t$pair[0][1]\t$pair[1][1]\t\n"
+;
        print OUT "$pair[0][0]\t$pair[1][0]\t$pair[0][1]\t$pair[1][1]\
+t\n";
    }
}
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Janitored by davido: Added code tags. Removed br tags from code.