I assume your input file is much biggger in reality otherwise I can't imagine this script taking a lot of time. In that case sorting the whole %query hash to only get the 5 highest might be slow

Instead you could use this:

my @result=([0,''],[0,''],[0,''],[0,''],[0,'']);
foreach (keys %query) {
  my $sw;
  my $n= [$query{$_},$_];
  if ($n->[0]>$result[4]) {
    if ($n->[0]>$result[3]) {
      if ($n->[0]>$result[2]) {      
        if ($n->[0]>$result[1]) {
          if ($n->[0]>$result[0]) {
            $sw=$result[0]; $result[0]=$n; $n=$sw;
          }
          $sw=$result[1]; $result[1]=$n; $n=$sw;
        }
        $sw=$result[2]; $result[2]=$n; $n=$sw;
      } 
      $sw=$result[3]; $result[3]=$n; $n=$sw;
    }
    $sw=$result[4]; $result[4]=$n; $n=$sw;
  }
}
print join("\n",map{$_->[1]},@result);
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The speedup of this somewhat ugly contraption lies in the expectation that the first 'if' will be true very very seldom for a big hash