Your problem is that you're calling nucleotide_count as a “class method”. More concretely, when you call a method like RECEIVER->method, the method call gets RECEIVER as its first argument. The nucleotide_count code expects an instance of class analysis (which would be a hashref), but instead it's getting the string analysis itself (which is not a hashref). To fix this, call my $thingy = analysis->new with appropriate arguments, and then use $thingy->nucleotide_count instead.

UPDATE: Oops, sorry, f00li5h beat me to it. Incidentally, note that good practice when posting questions like this is to try to strip the code down to as small as possible an example that still exhibits your error—it's a lot easier to get someone to look at 5 lines than a full program.