bio 0.7.0

data/lib/bio/io/higet.rb

@@ -0,0 +1,92 @@
+#
+# bio/io/higet.rb - SOAP interface for HGC HiGet
+#
+#   Copyright (C) 2005 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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
+#
+#  $Id: higet.rb,v 1.2 2005/09/26 13:00:08 k Exp $
+#
+
+require 'bio/io/soapwsdl'
+
+module Bio
+class HGC
+
+class HiGet < Bio::SOAPWSDL
+
+  SERVER_URI = "http://higet.hgc.jp/soap/higet.wsdl"
+
+  def initialize(wsdl = nil)
+    super(wsdl || SERVER_URI)
+  end
+
+  def higet_in_fasta(db, entries)
+    self.higet(db, entries, "-d fasta")
+  end
+
+  def higet_in_xml(db, entries)
+    self.higet(db, entries, "-d xml")
+  end
+
+end
+
+end # HGC
+end # Bio
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts ">>> Bio::HGC::HiGet"
+  serv = Bio::HGC::HiGet.new
+  serv.log = STDERR
+
+  puts "### HiFind"
+  puts serv.hifind("genbank", "human kinase", "-l 10")
+
+  puts "### HiGet"
+  puts serv.higet("genbank", "S40289", "")
+
+  puts "### HiGet (FASTA)"
+  puts serv.higet("genbank", "S40289", "-d fasta")
+
+  puts "### HiGet higet_in_fasta"
+  puts serv.higet_in_fasta("genbank", "S40289")
+
+  puts "### HiGet higet_in_xml"
+  puts serv.higet_in_xml("genbank", "S40289")
+
+end
+
+
+=begin
+
+= Bio::HGC::HiGet
+
+* ((<URL:http://higet.hgc.jp/>))
+
+== HiGet#hifind
+== HiGet#higet
+== HiGet#higet_in_fasta
+== HiGet#higet_in_xml
+
+=end
+

data/lib/bio/io/keggapi.rb

@@ -0,0 +1,863 @@
+#
+# bio/io/keggapi.rb - KEGG API access class
+#
+#   Copyright (C) 2003, 2004 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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
+#
+#  $Id: keggapi.rb,v 1.11 2005/12/18 19:10:55 k Exp $
+#
+
+require 'bio/io/soapwsdl'
+require 'uri'
+require 'net/http'
+
+module Bio
+class KEGG
+
+class API < Bio::SOAPWSDL
+
+  SERVER_URI = "http://soap.genome.jp/KEGG.wsdl"
+
+  def initialize(wsdl = nil)
+    @wsdl = wsdl || SERVER_URI
+    @log = nil
+    @start = 1
+    @max_results = 100
+    create_driver
+  end
+  attr_accessor :start, :max_results
+
+  def method_missing(*arg)
+    begin
+      results = @driver.send(*arg)
+    rescue Timeout::Error
+      retry
+    end
+    results = add_filter(results)
+    return results
+  end
+
+# def get_all_neighbors_by_gene(genes_id, org)
+#   get_all(:get_neighbors_by_gene, genes_id, org)
+# end
+
+  def get_all_best_best_neighbors_by_gene(genes_id)
+    get_all(:get_best_best_neighbors_by_gene, genes_id)
+  end
+
+  def get_all_best_neighbors_by_gene(genes_id)
+    get_all(:get_best_neighbors_by_gene, genes_id)
+  end
+
+  def get_all_reverse_best_neighbors_by_gene(genes_id)
+    get_all(:get_reverse_best_neighbors_by_gene, genes_id)
+  end
+
+  def get_all_paralogs_by_gene(genes_id)
+    get_all(:get_paralogs_by_gene, genes_id)
+  end
+
+  def get_all_genes_by_motifs(motif_id_list)
+    get_all(:get_genes_by_motifs, motif_id_list)
+  end
+
+  def get_all_oc_members_by_gene(genes_id)
+    get_all(:get_oc_members_by_gene, genes_id)
+  end
+
+  def get_all_pc_members_by_gene(genes_id)
+    get_all(:get_pc_members_by_gene, genes_id)
+  end
+
+  def get_all_genes_by_organism(org)
+    get_all(:get_genes_by_organism, org)
+  end
+
+  def get_all_linkdb_by_entry(entry_id, db)
+    get_all(:get_linkdb_by_entry, entry_id, db)
+  end
+
+
+  def save_image(url, filename = nil)
+    schema, user, host, port, reg, path, = URI.split(url)
+    filename ||= File.basename(path)
+
+    http = Net::HTTP.new(host, port)
+    response, = http.get(path)
+    File.open(filename, "w+") do |f|
+      f.print response.body
+    end
+    return filename
+  end
+
+
+  def get_entries(ary = [])
+    result = ''
+    step = [@max_results, 50].min
+    0.step(ary.length, step) do |i|
+      str = ary[i, step].join(" ")
+      if entry = @driver.send(:bget, str)
+        result << entry.to_s
+      end
+    end
+    return result
+  end
+
+  def get_aaseqs(ary = [])
+    result = ''
+    step = [@max_results, 50].min
+    0.step(ary.length, step) do |i|
+      str = "-f -n a " + ary[i, step].join(" ")
+      if entry = @driver.send(:bget, str)
+        result << entry.to_s
+      end
+    end
+    return result
+  end
+
+  def get_naseqs(ary = [])
+    result = ''
+    step = [@max_results, 50].min
+    0.step(ary.length, step) do |i|
+      str = "-f -n n " + ary[i, step].join(" ")
+      if entry = @driver.send(:bget, str)
+        result << entry.to_s
+      end
+    end
+    return result
+  end
+
+  def get_definitions(ary = [])
+    result = ''
+    step = [@max_results, 50].min
+    0.step(ary.length, step) do |i|
+      str = ary[i, step].join(" ")
+      if entry = @driver.send(:btit, str)
+        result << entry.to_s
+      end
+    end
+    return result
+  end
+
+
+  private
+
+  def add_filter(results)
+    if results.is_a?(Array)
+      results.each do |result|
+        def result.filter(fields)
+          fields.collect { |field| self.send(field) }
+        end
+      end
+    end
+    return results
+  end
+
+  def get_all(method, *args)
+    args << @start
+    args << @max_results
+
+    ary = []
+    loop do
+      results = @driver.send(method, *args)
+      break unless results
+      break if results.empty?
+      results = add_filter(results)
+      ary << results
+      args[-2] += @max_results  # next start count
+    end
+    return ary.flatten
+  end
+
+end # API
+
+end # KEGG
+end # Bio
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts ">>> KEGG API"
+  serv = Bio::KEGG::API.new
+# serv.log = STDERR
+
+  puts "--- parameters"
+  puts "        wsdl : #{serv.wsdl}"
+  puts "         log : #{serv.log}"
+  puts "       start : #{serv.start}"
+  puts " max_results : #{serv.max_results}"
+
+  puts "=== META"
+
+  puts "### list_databases"
+  list = serv.list_databases
+  list.each do |db|
+    print db.entry_id, "\t", db.definition, "\n"
+  end
+
+  puts "### list_organisms"
+  list = serv.list_organisms
+  list.each do |org|
+    print org.entry_id, "\t", org.definition, "\n"
+  end
+
+  puts "### list_pathways('map') : reference pathway"
+  list = serv.list_pathways("map")
+  list.each do |path|
+    print path.entry_id, "\t", path.definition, "\n"
+  end
+
+  puts "### list_pathways('eco') : E. coli pathway"
+  list = serv.list_pathways("eco")
+  list.each do |path|
+    print path.entry_id, "\t", path.definition, "\n"
+  end
+
+  puts "=== DBGET"
+
+  puts "### binfo('all')"
+  puts serv.binfo("all")
+
+  puts "### binfo('genbank')"
+  puts serv.binfo("genbank")
+
+  puts "### bfind('genbank kinase cell cycle human')"
+  puts serv.bfind("genbank kinase cell cycle human")
+
+  puts "### bget('gb:AJ617376')"
+  puts serv.bget("gb:AJ617376")
+
+  puts "### bget('eco:b0002 eco:b0003')"
+  puts serv.bget("eco:b0002 eco:b0003")
+
+  puts "### btit('eco:b0002 eco:b0003')"
+  puts serv.btit("eco:b0002 eco:b0003")
+
+  puts "--- get_entries(['eco:b0002', 'eco:b0003'])"
+  puts serv.get_entries(["eco:b0002", "eco:b0003"])
+
+  puts "--- get_aaseqs(['eco:b0002', 'eco:b0003'])"
+  puts serv.get_aaseqs(["eco:b0002", "eco:b0003"])
+
+  puts "--- get_naseqs(['eco:b0002', 'eco:b0003'])"
+  puts serv.get_naseqs(["eco:b0002", "eco:b0003"])
+
+  puts "--- get_definitions(['eco:b0002', 'eco:b0003'])"
+  puts serv.get_definitions(["eco:b0002", "eco:b0003"])
+
+  puts "--- get_definitions(('eco:b0001'..'eco:b0200').to_a)"
+  puts serv.get_definitions(("eco:b0001".."eco:b0200").to_a)
+
+  puts "=== LinkDB"
+
+  puts "### get_linkdb_by_entry('eco:b0002', 'pathway', 1, 5)"
+  list = serv.get_linkdb_by_entry("eco:b0002", "pathway", 1, 5)
+  list.each do |link|
+    puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
+  end
+
+  puts "--- get_all_linkdb_by_entry('eco:b0002', 'pathway')"
+  list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
+  list.each do |link|
+    puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
+  end
+
+  puts "=== SSDB"
+
+  puts "### get_neighbors_by_gene('eco:b0002', 'all', 1, 5)"
+  list = serv.get_neighbors_by_gene("eco:b0002", "all", 1, 5)
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "--- get_all_neighbors_by_gene('eco:b0002', 'bsu')"
+  list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "### get_best_best_neighbors_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 5)
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "--- get_all_best_best_neighbors_by_gene('eco:b0002')"
+  list = serv.get_all_best_best_neighbors_by_gene("eco:b0002")
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "### get_best_neighbors_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_best_neighbors_by_gene("eco:b0002", 1, 5)
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "--- get_all_best_neighbors_by_gene('eco:b0002')"
+  list = serv.get_all_best_neighbors_by_gene("eco:b0002")
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "### get_reverse_best_neighbors_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_reverse_best_neighbors_by_gene("eco:b0002", 1, 5)
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "--- get_all_reverse_best_neighbors_by_gene('eco:b0002')"
+  list = serv.get_all_reverse_best_neighbors_by_gene("eco:b0002")
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "### get_paralogs_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_paralogs_by_gene("eco:b0002", 1, 5)
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "--- get_all_paralogs_by_gene('eco:b0002')"
+  list = serv.get_all_paralogs_by_gene("eco:b0002")
+  list.each do |hit|
+    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
+  end
+
+  puts "### get_similarity_between_genes('eco:b0002', 'bsu:BG10350')"
+  relation = serv.get_similarity_between_genes("eco:b0002", "bsu:BG10350")
+  puts "        genes_id1 : #{relation.genes_id1}"		# string
+  puts "        genes_id2 : #{relation.genes_id2}"		# string
+  puts "         sw_score : #{relation.sw_score}"		# int
+  puts "        bit_score : #{relation.bit_score}"		# float
+  puts "         identity : #{relation.identity}"		# float
+  puts "          overlap : #{relation.overlap}"		# int
+  puts "  start_position1 : #{relation.start_position1}"	# int
+  puts "    end_position1 : #{relation.end_position1}"		# int
+  puts "  start_position2 : #{relation.start_position2}"	# int
+  puts "    end_position2 : #{relation.end_position2}"		# int
+  puts "   best_flag_1to2 : #{relation.best_flag_1to2}"		# boolean
+  puts "   best_flag_2to1 : #{relation.best_flag_2to1}"		# boolean
+  puts "      definition1 : #{relation.definition1}"		# string
+  puts "      definition2 : #{relation.definition2}"		# string
+  puts "          length1 : #{relation.length1}"		# int
+  puts "          length2 : #{relation.length2}"		# int
+
+  puts "=== MOTIF"
+
+  puts "### get_motifs_by_gene('eco:b0002', 'pfam')"
+  list = serv.get_motifs_by_gene("eco:b0002", "pfam")
+  list.each do |motif|
+    puts motif.motif_id
+  end if list
+
+  puts "### get_motifs_by_gene('eco:b0002', 'tfam')"
+  list = serv.get_motifs_by_gene("eco:b0002", "tfam")
+  list.each do |motif|
+    puts motif.motif_id
+  end if list
+
+  puts "### get_motifs_by_gene('eco:b0002', 'pspt')"
+  list = serv.get_motifs_by_gene("eco:b0002", "pspt")
+  list.each do |motif|
+    puts motif.motif_id
+  end if list
+
+  puts "### get_motifs_by_gene('eco:b0002', 'pspf')"
+  list = serv.get_motifs_by_gene("eco:b0002", "pspf")
+  list.each do |motif|
+    puts motif.motif_id
+  end if list
+
+  puts "### get_motifs_by_gene('eco:b0002', 'all')"
+  list = serv.get_motifs_by_gene("eco:b0002", "all")
+  list.each do |motif|
+    puts "--- motif result"
+    puts "       motif_id : #{motif.motif_id}"
+    puts "     definition : #{motif.definition}"
+    puts "       genes_id : #{motif.genes_id}"
+    puts " start_position : #{motif.start_position}"
+    puts "   end_position : #{motif.end_position}"
+    puts "          score : #{motif.score}"
+    puts "         evalue : #{motif.evalue}"
+  end
+
+  puts "### get_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'], 1, 5)"
+  list = serv.get_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"], 1, 5)
+  list.each do |gene|
+    puts [ gene.entry_id, gene.definition ].join("\t")
+  end
+
+  puts "--- get_all_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'])"
+  list = serv.get_all_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"])
+  list.each do |gene|
+    puts [ gene.entry_id, gene.definition ].join("\t")
+  end
+
+  puts "=== KO, OC, PC"
+
+  puts "### get_ko_by_gene('eco:b0002')"
+  list = serv.get_ko_by_gene("eco:b0002")
+  list.each do |ko|
+    puts ko
+  end
+
+  puts "### get_ko_members('ko:K00003')"
+  list = serv.get_ko_members("ko:K00003")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "### get_oc_members_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_oc_members_by_gene("eco:b0002", 1, 5)
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "--- get_all_oc_members_by_gene('eco:b0002')"
+  list = serv.get_all_oc_members_by_gene("eco:b0002")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "### get_pc_members_by_gene('eco:b0002', 1, 5)"
+  list = serv.get_pc_members_by_gene("eco:b0002", 1, 5)
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "--- get_all_pc_members_by_gene('eco:b0002')"
+  list = serv.get_all_pc_members_by_gene("eco:b0002")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "=== PATHWAY"
+
+  puts "==== coloring pathway"
+
+  puts "### mark_pathway_by_objects('path:eco00260', obj_list)"
+  puts "  obj_list = ['eco:b0002', 'cpd:C00263']"
+  obj_list = ["eco:b0002", "cpd:C00263"]
+  url = serv.mark_pathway_by_objects("path:eco00260", obj_list)
+  puts url
+
+  puts "### color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)"
+  puts "  obj_list = ['eco:b0207', 'eco:b1300']"
+  puts "  fg_list  = ['blue', '#00ff00']"
+  puts "  bg_list  = ['#ff0000', 'yellow']"
+  obj_list = ["eco:b0207", "eco:b1300"]
+  fg_list  = ["blue", "#00ff00"]
+  bg_list  = ["#ff0000", "yellow"]
+  url = serv.color_pathway_by_objects("path:eco00053", obj_list, fg_list, bg_list)
+  puts url
+
+  #puts "--- save_image(#{url})"
+  #filename = serv.save_image(url, "test.gif")
+  #filename = serv.save_image(url)
+  #puts filename
+
+  puts "==== objects on pathway"
+
+  puts "### get_genes_by_pathway('path:map00010')"
+  list = serv.get_genes_by_pathway("path:map00010")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "### get_genes_by_pathway('path:eco00010')"
+  list = serv.get_genes_by_pathway("path:eco00010")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "### get_enzymes_by_pathway('path:map00010')"
+  list = serv.get_enzymes_by_pathway("path:map00010")
+  list.each do |enzyme|
+    puts enzyme
+  end
+
+  puts "### get_enzymes_by_pathway('path:eco00010')"
+  list = serv.get_enzymes_by_pathway("path:eco00010")
+  list.each do |enzyme|
+    puts enzyme
+  end
+
+  puts "### get_compounds_by_pathway('path:map00010')"
+  list = serv.get_compounds_by_pathway("path:map00010")
+  list.each do |compound|
+    puts compound
+  end
+
+  puts "### get_compounds_by_pathway('path:eco00010')"
+  list = serv.get_compounds_by_pathway("path:eco00010")
+  list.each do |compound|
+    puts compound
+  end
+
+  puts "### get_reactions_by_pathway('path:map00010')"
+  list = serv.get_reactions_by_pathway("path:map00010")
+  list.each do |reaction|
+    puts reaction
+  end
+
+  puts "### get_reactions_by_pathway('path:eco00010')"
+  list = serv.get_reactions_by_pathway("path:eco00010")
+  list.each do |reaction|
+    puts reaction
+  end
+
+  puts "==== pathway by objects"
+
+  puts "### get_pathways_by_genes(['eco:b0756', 'eco:b1002'])"
+  list = serv.get_pathways_by_genes(["eco:b0756", "eco:b1002"])
+  list.each do |path|
+    puts path
+  end
+
+  puts "### get_pathways_by_enzymes(['ec:5.1.3.3', 'ec:3.1.3.10'])"
+  list = serv.get_pathways_by_enzymes(["ec:5.1.3.3", "ec:3.1.3.10"])
+  list.each do |path|
+    puts path
+  end
+
+  puts "### get_pathways_by_compounds(['cpd:C00221', 'cpd:C00267'])"
+  list = serv.get_pathways_by_compounds(["cpd:C00221", "cpd:C00267"])
+  list.each do |path|
+    puts path
+  end
+
+  puts "### get_pathways_by_reactions(['rn:R00014', 'rn:R00710'])"
+  list = serv.get_pathways_by_reactions(["rn:R00014", "rn:R00710"])
+  list.each do |path|
+    puts path
+  end
+
+  puts "==== relation between objects"
+
+  puts "### get_linked_pathways('path:eco00620')"
+  list = serv.get_linked_pathways('path:eco00620')
+  list.each do |path|
+    puts path
+  end
+
+  puts "### get_genes_by_enzyme('ec:1.1.1.1', 'eco')"
+  list = serv.get_genes_by_enzyme("ec:1.1.1.1", "eco")
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "### get_enzymes_by_gene('eco:b0002')"
+  list = serv.get_enzymes_by_gene("eco:b0002")
+  list.each do |enzyme|
+    puts enzyme
+  end
+
+  puts "### get_enzymes_by_compound('cpd:C00345')"
+  list = serv.get_enzymes_by_compound("cpd:C00345")
+  list.each do |enzyme|
+    puts enzyme
+  end
+
+  puts "### get_enzymes_by_reaction('rn:R00100')"
+  list = serv.get_enzymes_by_reaction("rn:R00100")
+  list.each do |enzyme|
+    puts enzyme
+  end
+
+  puts "### get_compounds_by_enzyme('ec:2.7.1.12')"
+  list = serv.get_compounds_by_enzyme("ec:2.7.1.12")
+  list.each do |compound|
+    puts compound
+  end
+
+  puts "### get_compounds_by_reaction('rn:R00100')"
+  list = serv.get_compounds_by_reaction("rn:R00100")
+  list.each do |compound|
+    puts compound
+  end
+  
+  puts "### get_reactions_by_enzyme('ec:2.7.1.12')"
+  list = serv.get_reactions_by_enzyme("ec:2.7.1.12")
+  list.each do |reaction|
+    puts reaction
+  end
+
+  puts "### get_reactions_by_compound('cpd:C00199')"
+  list = serv.get_reactions_by_compound("cpd:C00199")
+  list.each do |reaction|
+    puts reaction
+  end
+  
+  puts "=== GENES"
+
+  puts "### get_genes_by_organism('mge', 1, 5)"
+  list = serv.get_genes_by_organism("mge", 1, 5)
+  list.each do |gene|
+    puts gene
+  end
+
+  puts "--- get_all_genes_by_organism('mge')"
+  list = serv.get_all_genes_by_organism("mge")
+  list.each do |gene|
+    puts gene
+  end
+  
+  puts "=== GENOME"
+
+  puts "### get_number_of_genes_by_organism(org)"
+  puts serv.get_number_of_genes_by_organism("mge")
+
+end
+
+
+=begin
+
+= Bio::KEGG::API
+
+KEGG API is a web service to use KEGG system via SOAP/WSDL.  For more
+informations on KEGG API, see the following site and its reference manual.
+
+  * ((<URL:http://www.genome.jp/kegg/soap/>))
+
+--- Bio::KEGG::API.new(wsdl = nil)
+
+Connect to the KEGG API's SOAP server.  A WSDL file will be automatically
+downloaded and parsed to generate the SOAP client driver.  The default URL
+for the WSDL is http://soap.genome.jp/KEGG.wsdl but it can be changed by
+the argument or by wsdl= method.
+
+--- Bio::KEGG::API#wsdl
+
+Returns URL of the current WSDL file.
+
+--- Bio::KEGG::API#wsdl=(url)
+
+Change the URL for WSDL file of the KEGG API if needed for some reason:
+
+  serv = Bio::KEGG::API.new("http://133.103.100.186/KEGG.wsdl")
+
+or
+
+  serv = Bio::KEGG::API.new
+  serv.wsdl = "http://133.103.100.186/KEGG.wsdl"
+
+note that both can't read two or more different WSDL files.
+
+--- Bio::KEGG::API#log
+
+Returns current logging IO.
+
+--- Bio::KEGG::API#log=(io)
+
+Change the IO for logging.  The argument is passed to wiredump_dev method
+of the SOAP4R, thus
+
+  serv = Bio::KEGG::API.new
+  serv.log = STDERR
+
+will print all the SOAP transactions in standard error.
+This feature is especially useful for debug.
+
+--- Bio::KEGG::API#start
+
+Returns current value for the 'start' count for the methods having 
+start/max_results argument pairs.
+
+--- Bio::KEGG::API#start=(number)
+
+Changes the default value for the 'start' count.
+
+--- Bio::KEGG::API#max_results
+
+Returns current value for the 'max_results' number for the methods having 
+start/max_results argument pairs.
+
+--- Bio::KEGG::API#max_results=(number)
+
+Changes the default value for the 'max_results' count.
+If your request timeouts, try smaller value for the max_results.
+
+=== KEGG API methods implemented only in BioRuby
+
+In BioRuby, returned values are added filter method to pick up
+values in a complex data type as an array.
+
+  #!/usr/bin/env ruby
+
+  require 'bio'
+
+  serv = Bio::KEGG::API.new
+  results = serv.get_best_neighbors_by_gene("eco:b0002", "bsu")
+
+  # case 0 : without filter
+  results.each do |hit|
+    print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+  end
+
+  # case 1 : select gene names and SW score only
+  fields = [:genes_id1, :genes_id2, :sw_score]
+  results.each do |hit|
+    puts hit.filter(fields).join("\t")
+  end
+  
+  # case 2 : also uses aligned position in each amino acid sequence etc.
+  fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2]
+  fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1]
+  results.each do |hit|
+    print "> score: ", hit.sw_score, ", identity: ", hit.identity, "\n"
+    print "1:\t", hit.filter(fields1).join("\t"), "\n"
+    print "2:\t", hit.filter(fields2).join("\t"), "\n"
+  end
+
+Using filter method will make it easy to change fields to select and
+keep the script clean.
+
+
+--- Bio::KEGG::API#get_all_neighbors_by_gene(genes_id, org)
+--- Bio::KEGG::API#get_all_best_best_neighbors_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_best_neighbors_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_reverse_best_neighbors_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_paralogs_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_genes_by_motifs(motif_id_list)
+--- Bio::KEGG::API#get_all_oc_members_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_pc_members_by_gene(genes_id)
+--- Bio::KEGG::API#get_all_genes_by_organism(org)
+
+These methods are wrapper for the methods without _all_ in its name
+and internally iterate to retrive all the results using start/max_results
+value pairs described above.  For example,
+
+  #!/usr/bin/env ruby
+  
+  require 'soap/wsdlDriver'
+  
+  wsdl = "http://soap.genome.jp/KEGG.wsdl"
+  serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
+  serv.generate_explicit_type = true
+  
+  start = 1
+  max_results = 100
+  
+  loop do
+    results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
+    break unless results	# when no more results returned
+    results.each do |hit|
+      print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+    end
+    start += max_results
+  end
+
+can be witten as
+
+  #!/usr/bin/env ruby
+  
+  require 'bio'
+  
+  serv = Bio::KEGG::API.new
+  
+  results = serv.get_all_best_neighbors_by_gene('eco:b0002')
+  results.each do |hit|
+    print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+  end
+
+
+--- Bio::KEGG::API#save_image(url, filename = nil)
+
+Some methods of the KEGG API will return a URL of the generated image.
+This method save an image specified by the URL.  The filename can be
+specified by its second argument, otherwise basename of the URL will
+be used.
+
+  #!/usr/bin/env ruby
+  
+  require 'bio'
+  
+  serv = Bio::KEGG::API.new("http://soap.genome.jp/v3.0/KEGG.wsdl")
+  
+  list = ["eco:b1002", "eco:b2388"]
+  url = serv.mark_pathway_by_objects("path:eco00010", list)
+  
+  # Save with the original filename (eco00010.gif in this case)
+  serv.save_image(url)
+
+  # or save as "save_image.gif"
+  serv.save_image(url, "save_image.gif")
+
+--- Bio::KEGG::API#get_entries(entry_id_list)
+--- Bio::KEGG::API#get_aaseqs(entry_id_list)
+--- Bio::KEGG::API#get_naseqs(entry_id_list)
+--- Bio::KEGG::API#get_definitions(entry_id_list)
+
+For the shortcut and backward compatibility.
+
+
+=== General KEGG API methods
+
+For the methods listed below, consult the KEGG API manual at
+
+  * ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>))
+
+--- list_databases
+--- list_organisms
+--- list_pathways(org)
+--- binfo(string)
+--- bget(string)
+--- bfind(string)
+--- btit(string)
+--- get_linkdb_by_entry(entry_id, db, start, max_results)
+#--- get_neighbors_by_gene(genes_id, org, 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_similarity_between_genes(genes_id1, genes_id2)
+--- 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_members(ko_id)
+--- 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_genes_by_pathway(pathway_id)
+--- get_enzymes_by_pathway(pathway_id)
+--- get_compounds_by_pathway(pathway_id)
+--- get_reactions_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_reactions(reaction_id_list)
+--- 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_reaction(reaction_id)
+--- get_compounds_by_enzyme(enzyme_id)
+--- get_compounds_by_reaction(reaction_id)
+--- get_reactions_by_enzyme(enzyme_id)
+--- get_reactions_by_compound(compound_id)
+--- get_genes_by_organism(org, start, max_results)
+--- get_number_of_genes_by_organism(org)                             
+
+=end
+