Ok thanks a ton.. so let me clarify to see if I get it... in this situation based on what you said : 
 
 foreach my $key1 ( sort keys %genes ) {
     print "\t". scalar (keys %{$genes{$key1}}) . "\t";
          foreach my $key2 ( sort keys %{$genes{$key1}} ) { etc....

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I am printing the number of hash keys at the $gene{$r4} level...... and the %{} is a wrapper that turns a hash reference into a hash? ( as opposed to above where its an @ ref into an @. So changing that reference to an actual hash allows me to see the true values of the keys ( or in this instance the number of them because of the scalar command) rather then seeing the hash reference? If the wrapper were not to be there and I tried to access a deeper level in the hash rather then just printing the values at that level, it wouldn't work because the values themselves don't store the information for the overall nested structure (thats what the refs are for) ..correct?

In reply to Re^2: Hash of Hash of Array Syntax help by ZWcarp
in thread Hash of Hash of Array Syntax help by ZWcarp

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