[BioRuby-cvs] bioruby/lib/bio/shell/plugin keggapi.rb,NONE,1.1

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv329/lib/bio/shell/plugin

Added Files:
	keggapi.rb 
Log Message:
* start


--- NEW FILE: keggapi.rb ---
#
# = bio/shell/plugin/obda.rb - plugin for OBDA
#
# Copyright::	Copyright (C) 2005
#		Toshiaki Katayama <k at bioruby.org>
# Lisence::	LGPL
#
# $Id: keggapi.rb,v 1.1 2005/11/05 10:58:01 k Exp $
#
#--
#
#  This library is free software; you can redistribute it and/or
#  modify it under the terms of the GNU Lesser General Public
#  License as published by the Free Software Foundation; either
#  version 2 of the License, or (at your option) any later version.
#
#  This library is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#  Lesser General Public License for more details.
#
#  You should have received a copy of the GNU Lesser General Public
#  License along with this library; if not, write to the Free Software
#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
#
#++
#

require 'bio/io/soapwsdl'

module Bio::Shell

  private

  def setup_keggapi
    unless @keggapi
      @keggapi = Bio::SOAPWSDL.new("http://soap.genome.jp/KEGG.wsdl")
    end
  end

  def bfind(str)
    setup_keggapi
    result = @keggapi.bfind(str)
    display result
    return result
  end

  def bget(str)
    setup_keggapi
    entry = @keggapi.bget(str)
    if block_given?
      yield entry
    else
      display entry
    end
    return entry
  end

end

=begin
--- list_databases
--- list_organisms
--- list_pathways(org)
--- binfo(string)
--- bfind(string)
--- bget(string)
--- btit(string)
--- get_linkdb_by_entry(entry_id, db, start, max_results)
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
--- get_best_neighbors_by_gene(genes_id, start, max_results)
--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
--- get_paralogs_by_gene(genes_id, start, max_results)
--- get_motifs_by_gene(genes_id, db)
--- get_genes_by_motifs(motif_id_list, start, max_results)
--- get_ko_by_gene(genes_id)
--- get_ko_by_ko_class(ko_class_id)
--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
--- get_genes_by_ko(ko_id, org)
--- get_oc_members_by_gene(genes_id, start, max_results)
--- get_pc_members_by_gene(genes_id, start, max_results)
--- mark_pathway_by_objects(pathway_id, object_id_list)
--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
--- get_genes_by_pathway(pathway_id)
--- get_enzymes_by_pathway(pathway_id)
--- get_compounds_by_pathway(pathway_id)
--- get_glycans_by_pathway(pathway_id)
--- get_reactions_by_pathway(pathway_id)
--- get_kos_by_pathway(pathway_id)
--- get_pathways_by_genes(genes_id_list)
--- get_pathways_by_enzymes(enzyme_id_list)
--- get_pathways_by_compounds(compound_id_list)
--- get_pathways_by_glycans(glycan_id_list)
--- get_pathways_by_reactions(reaction_id_list)
--- get_pathways_by_kos(ko_id_list, org)
--- get_linked_pathways(pathway_id)
--- get_genes_by_enzyme(enzyme_id, org)
--- get_enzymes_by_gene(genes_id)
--- get_enzymes_by_compound(compound_id)
--- get_enzymes_by_glycan(glycan_id)
--- get_enzymes_by_reaction(reaction_id)
--- get_compounds_by_enzyme(enzyme_id)
--- get_compounds_by_reaction(reaction_id)
--- get_glycans_by_enzyme(enzyme_id)
--- get_glycans_by_reaction(reaction_id)
--- get_reactions_by_enzyme(enzyme_id)
--- get_reactions_by_compound(compound_id)
--- get_reactions_by_glycan(glycan_id)
--- get_genes_by_organism(org, start, max_results)
--- get_number_of_genes_by_organism(org)
--- convert_mol_to_kcf(mol_text)
=end