[BioRuby-cvs] bioruby/lib/bio/io keggapi.rb,1.12,1.13
Katayama Toshiaki
k at dev.open-bio.org
Tue Sep 19 05:45:50 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv31383/lib/bio/io
Modified Files:
keggapi.rb
Log Message:
* documentations are moved to RDoc
Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/keggapi.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** keggapi.rb 14 Jul 2006 14:48:56 -0000 1.12
--- keggapi.rb 19 Sep 2006 05:45:48 -0000 1.13
***************
*** 1,22 ****
#
! # bio/io/keggapi.rb - KEGG API access class
! #
! # Copyright (C) 2003, 2004 KATAYAMA Toshiaki <k at 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
#
! # $Id$
#
--- 1,9 ----
#
! # = bio/io/keggapi.rb - KEGG API access class
#
! # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
! # $Id$
#
***************
*** 29,36 ****
--- 16,197 ----
class KEGG
+ # == Description
+ #
+ # KEGG API is a web service to use KEGG system via SOAP/WSDL.
+ #
+ # == References
+ #
+ # For more informations on KEGG API, see the following site and read the
+ # reference manual.
+ #
+ # * http://www.genome.jp/kegg/soap/
+ # * http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
+ #
+ # == List of methods
+ #
+ # As of KEGG API v5.0
+ #
+ # * 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_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)
+ #
+ # == 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)
+ #
+ # These methods are for the shortcut and backward compatibility
+ # (these methods existed in the older version of the KEGG API).
+ #
class API < Bio::SOAPWSDL
SERVER_URI = "http://soap.genome.jp/KEGG.wsdl"
+ # 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.
def initialize(wsdl = nil)
@wsdl = wsdl || SERVER_URI
***************
*** 40,44 ****
create_driver
end
! attr_accessor :start, :max_results
def method_missing(*arg)
--- 201,215 ----
create_driver
end
!
! # Returns current value for the 'start' count for the methods having
! # start/max_results argument pairs or changes the default value for
! # the 'start' count.
! attr_accessor :start
!
! # Returns current value for the 'max_results' number for the methods having
! # start/max_results argument pairs or changes the default value for the
! # 'max_results' count. If your request timeouts, try smaller value for
! # the max_results.
! attr_accessor :max_results
def method_missing(*arg)
***************
*** 52,55 ****
--- 223,227 ----
end
+
# def get_all_neighbors_by_gene(genes_id, org)
# get_all(:get_neighbors_by_gene, genes_id, org)
***************
*** 202,206 ****
# serv.log = STDERR
! puts "--- parameters"
puts " wsdl : #{serv.wsdl}"
puts " log : #{serv.log}"
--- 374,378 ----
# serv.log = STDERR
! puts "# * parameters"
puts " wsdl : #{serv.wsdl}"
puts " log : #{serv.log}"
***************
*** 254,270 ****
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)
--- 426,442 ----
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)
***************
*** 277,281 ****
end
! puts "--- get_all_linkdb_by_entry('eco:b0002', 'pathway')"
list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
list.each do |link|
--- 449,453 ----
end
! puts "# * get_all_linkdb_by_entry('eco:b0002', 'pathway')"
list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
list.each do |link|
***************
*** 291,295 ****
end
! puts "--- get_all_neighbors_by_gene('eco:b0002', 'bsu')"
list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
list.each do |hit|
--- 463,467 ----
end
! puts "# * get_all_neighbors_by_gene('eco:b0002', 'bsu')"
list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
list.each do |hit|
***************
*** 303,307 ****
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|
--- 475,479 ----
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|
***************
*** 315,319 ****
end
! puts "--- get_all_best_neighbors_by_gene('eco:b0002')"
list = serv.get_all_best_neighbors_by_gene("eco:b0002")
list.each do |hit|
--- 487,491 ----
end
! puts "# * get_all_best_neighbors_by_gene('eco:b0002')"
list = serv.get_all_best_neighbors_by_gene("eco:b0002")
list.each do |hit|
***************
*** 327,331 ****
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|
--- 499,503 ----
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|
***************
*** 339,343 ****
end
! puts "--- get_all_paralogs_by_gene('eco:b0002')"
list = serv.get_all_paralogs_by_gene("eco:b0002")
list.each do |hit|
--- 511,515 ----
end
! puts "# * get_all_paralogs_by_gene('eco:b0002')"
list = serv.get_all_paralogs_by_gene("eco:b0002")
list.each do |hit|
***************
*** 393,397 ****
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}"
--- 565,569 ----
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}"
***************
*** 409,413 ****
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|
--- 581,585 ----
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|
***************
*** 435,439 ****
end
! puts "--- get_all_oc_members_by_gene('eco:b0002')"
list = serv.get_all_oc_members_by_gene("eco:b0002")
list.each do |gene|
--- 607,611 ----
end
! puts "# * get_all_oc_members_by_gene('eco:b0002')"
list = serv.get_all_oc_members_by_gene("eco:b0002")
list.each do |gene|
***************
*** 447,451 ****
end
! puts "--- get_all_pc_members_by_gene('eco:b0002')"
list = serv.get_all_pc_members_by_gene("eco:b0002")
list.each do |gene|
--- 619,623 ----
end
! puts "# * get_all_pc_members_by_gene('eco:b0002')"
list = serv.get_all_pc_members_by_gene("eco:b0002")
list.each do |gene|
***************
*** 473,477 ****
puts url
! #puts "--- save_image(#{url})"
#filename = serv.save_image(url, "test.gif")
#filename = serv.save_image(url)
--- 645,649 ----
puts url
! #puts "# * save_image(#{url})"
#filename = serv.save_image(url, "test.gif")
#filename = serv.save_image(url)
***************
*** 618,622 ****
end
! puts "--- get_all_genes_by_organism('mge')"
list = serv.get_all_genes_by_organism("mge")
list.each do |gene|
--- 790,794 ----
end
! puts "# * get_all_genes_by_organism('mge')"
list = serv.get_all_genes_by_organism("mge")
list.each do |gene|
***************
*** 631,864 ****
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
-
--- 803,804 ----
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