Bug - Bio::Fetch.query about bioruby HOT 3 CLOSED

Try this:

server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
server.fetch('hal', 'VNG1467G')

I proposed a change here

from bioruby.

Thanks for reporting.

After BioRuby 1.5, default server URL is removed from Bio::Fetch.new, and the Bio::Fetch.query method is removed.

One of alternatives is Bio::Fetch::EBI.query which uses EBI Dbfetch server. However, as far as I know, KEGG GENES entries cannot be retrieved by using EBI Dbfetch.

To get KEGG GENES, Bio::TogoWS::REST can be used.

  require 'bio'
  entry = Bio::TogoWS::REST.entry("kegg-genes", "hal:VNG1467G")

from bioruby.

related pull request: #77

from bioruby.