I stored the data in an array instead:

#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

use List::Util qw{ uniq };

my @genes;
while (<>) {
    my ($id, $type, $value) = (split)[ 0, 3, 4 ];
    push @genes, [ $id, $type, $value ];
}

my @types = sort +uniq(map $_->[1], @genes);

say join "\t", 'Gene', @types;
for my $gene (@genes) {
    say join "\t", $gene->[0], map $_ eq $gene->[1] ? $gene->[2] : q()
+, @types;
}
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]