[BioRuby] Remove broken Bio.method_missing

[Naohisa Goto]

Hi all,

There is Bio.method_missing, the hook of undefined methods. In the
existing code, Bio::Shell method corresponding to the given method
name is called. The expected behavior is to provide shortcut of
Bio::Shell methods with shorter name without typing "Shell".
However, currently, most methods raises error, partly due to the
bypass of initialization procedure.

Our experience of writing and using BioRuby suggests that the use
of method_missing should normally be avoided unless it is really
necessary, partly because it tends to cause catastrophe especially
when an exception is raised. In the case of Bio.method_missing,
I think it is not necessary to use the method here.

So, I remove Bio.method_missing. Alternatively, use Bio::Shell.xxxxx
(xxxxx is a method name).
-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org