[BioRuby] Removal of Bio::DBGET and Bio::Ensembl wihch use discontinued API

Naohisa Goto ngoto at gen-info.osaka-u.ac.jp
Mon Sep 3 08:10:12 UTC 2012


Hi all,

I'd like to remove the following two old obsolete classes that use
discontinued API access via the internet.

Bio::DBGET in bio/io/dbget.rb (and sample/dbget):
Reason: It does not work because it uses old original protocol that
was discontinued about 8 years ago.
Alternatives: The DBGET system is still available via the web.
http://www.genome.jp/en/gn_dbget.html
However, no API code is written in Ruby.

Bio::Ensembl in bio/io/ensembl.rb (and test codes):
Reason: It does not work after the renewal of Ensembl web site in 2008.
Alternatives: bio-ensembl gem which supports current ensembl API.
http://rubygems.org/gems/bio-ensembl

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




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