$h->{"5p-tR-halves"} += $line[ 1] / $reads * 1000000;
            $h->{"5p-tRFs"}      += $line[ 3] / $reads * 1000000;
            $h->{"3p-tR-halves"} += $line[ 5] / $reads * 1000000;
            $h->{"3p-CCA-tRFs"}  += $line[ 7] / $reads * 1000000;
            $h->{"3p-tRFs"}      += $line[ 9] / $reads * 1000000;
            $h->{"tRF-1"}        += $line[11] / $reads * 1000000;
            $h->{"tRNA-leader"}  += $line[13] / $reads * 1000000;
            $h->{"misc-tRFs"}    += $line[15] / $reads * 1000000;
[download]

Years ago that would not have bothered me but nowadays it makes me twitch. YMMV but for DRY:

my $i = 1;
for (qw/5p-tR-halves 5p-tRFs 3p-tR-halves 3p-CCA-tRFs 3p-tRFs tRF-1 tR
+NA-leader misc-tRFs/) {
    $->{$_} += $line[$i] / $reads * 1000000;
    $i += 2; # Odd entries only
}
[download]