Do you mean that when you do this step:

   my $tag = $f->primary_tag;
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the value of $tag is one of: CDS, exons, genes, mRNAs, misc_RNAs, primer_binds, repeat_regions, or sources?

If that's what is happening, all you need to do is place a condition on the following "push" -- only do the push if the value of $tag is one that you want:

    push @{$sorted_features{$tag}}, $f if ($tag =~ /CDS|genes|primer_b
+inds|sources/);
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Or, if you prefer, you can create a hash whose keys are the desired set of feature names, and then the condition can check for the hash key, instead of doing a regex match:

my %sorted_features;
my %want = map { $_ => 1 } qw/CDS genes primer_binds sources/;
for my $f ( @features ) {
    my $tag = $f->primary_tag;
    push @{$sorted_features{$tag}}, $f if( $want{$tag} );
}
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