[BioRuby] Remove classes that does not work: Bio::NCBI::SOAP, Bio::KEGG::Taxonomy

[Naohisa Goto]

Hi all,

I'd like to remove the following two classes that are currently broken
and I think there are no hope to be fixed.

Bio::NCBI::SOAP
Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) always raises error during the
parsing of WSDL files provided by NCBI. The error occurrs both with Ruby
1.8.X (with bundled SOAP4R) and Ruby 1.9.X (with soap4r-ruby1.9 gem). To
solve the error, modifying SOAP4R may be needed. I think it is difficult.
Fortunately, there is already an alternative class Bio::NCBI::REST, REST
client class for NCBI EUtil web services.

Bio::KEGG::Taxonomy
Bio::KEGG::Taxonomy (in lib/bio/db/kegg/taxonomy.rb) raises error or the
returned data seems to be broken. Running the sample script
sample/demo_kegg_taxonomy.rb shows error or falls into infinite loop.
Moreover, KEGG closes public FTP site and the file "taxonomy" can only
be obtained by paid subscribers. So, I can not test the class with the
latest data and thus I give up fixing.

Of course, patches to solve the above problems are welcome.

-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org