bio 1.4.3.0001 → 1.5.0

data/lib/bio/io/keggapi.rb

@@ -1,363 +0,0 @@
-#
-# = bio/io/keggapi.rb - KEGG API access class
-#
-# Copyright::  Copyright (C) 2003, 2004 Toshiaki Katayama <k@bioruby.org>
-# License::    The Ruby License
-#
-# $Id:$
-#
-
-require 'bio/io/soapwsdl'
-require 'uri'
-require 'net/http'
-require 'bio/command'
-
-module Bio
-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
-    @log = nil
-    @start = 1
-    @max_results = 100
-    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)
-    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 = Bio::Command.new_http(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|
-	next if result.is_a?(Fixnum)
-        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
-

data/lib/bio/io/ncbisoap.rb

@@ -1,156 +0,0 @@
-#
-# = bio/io/ncbisoap.rb - SOAP interface for NCBI Entrez Utilities
-#
-# Copyright::   Copyright (C) 2004, 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-require 'bio/io/ncbirest'
-require 'bio/io/soapwsdl'
-
-module Bio
-class NCBI
-
-# == References
-#
-# * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html
-#
-# == Methods
-#
-# All methods accept a hash as its argument and most of the keys can be
-# ommited (values are string).
-#
-# Note: Methods which name ends with _MS are designed for use with
-# Microsoft Visual Studio and SOAP Toolkit 3.0
-#
-# * http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_ms_help.html
-#
-# * run_eFetch(_MS)
-#   * "db", "id", "WebEnv", "query_key", "tool", "email", "retstart",
-#     "retmax", "rettype", "strand", "seq_start", "seq_stop", "complexity",
-#     "report" 
-#
-# * run_eGquery(_MS)
-#   * "term", "tool", "email"
-#
-# * run_eInfo(_MS)
-#   * "db", "tool", "email"
-#
-# * run_eSpell(_MS)
-#   * "db", "term", "tool", "email"
-#
-# * run_eLink(_MS)
-#   * "db", "id", "reldate", "mindate", "maxdate", "datetype", "term"
-#     "dbfrom", "WebEnv", "query_key", "cmd", "tool", "email"
-#
-# * run_eSearch(_MS)
-#   * "db", "term", "WebEnv", "QueryKey", "usehistory", "tool", "email",
-#     "field", "reldate", "mindate", "maxdate", "datetype", "RetStart",
-#     "RetMax", "rettype", "sort"
-#
-# * run_eSummary(_MS)
-#   * "db", "id", "WebEnv", "query_key", "retstart", "retmax", "tool", "email"
-#
-# == Complex data types
-#
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/egquery.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/einfo.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/esearch.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/esummary.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/elink.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/efetch.xsd
-# * http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/espell.xsd
-#
-class SOAP < Bio::SOAPWSDL
-
-  BASE_URI = "http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
-
-  # set default to EUtils
-  SERVER_URI = BASE_URI + "eutils.wsdl"
-
-  def initialize(wsdl = nil)
-    super(wsdl || self.class::SERVER_URI)
-  end
-
-  def method_missing(*arg)
-    sleep 3			# make sure to rest for 3 seconds per request
-    @driver.send(*arg)
-  end
-
-  class EUtils < Bio::NCBI::SOAP
-    SERVER_URI = BASE_URI + "eutils.wsdl"
-  end
-
-  class EUtilsLite < Bio::NCBI::SOAP
-    SERVER_URI = BASE_URI + "eutils_lite.wsdl"
-  end
-
-  class EFetch < Bio::NCBI::SOAP
-    SERVER_URI = BASE_URI + "efetch.wsdl"
-  end
-
-  class EFetchLite < Bio::NCBI::SOAP
-    SERVER_URI = BASE_URI + "efetch_lit.wsdl"
-  end
-
-end # SOAP
-end # NCBI
-end # Bio
-
-
-if __FILE__ == $0
-
-  puts ">>> Bio::NCBI::SOAP::EFetch"
-  efetch = Bio::NCBI::SOAP::EFetch.new
-
-  puts "### run_eFetch in EFetch"
-  hash = {"db" => "protein", "id" => "37776955"}
-  result = efetch.run_eFetch(hash)
-  p result
-
-  puts ">>> Bio::NCBI::SOAP::EUtils"
-  eutils = Bio::NCBI::SOAP::EUtils.new
-
-  puts "### run_eFetch in EUtils"
-  hash = {"db" => "pubmed", "id" => "12345"}
-  result = eutils.run_eFetch(hash)
-  p result
-
-  puts "### run_eGquery - Entrez meta search to count hits in each DB"
-  hash = {"term" => "kinase"}
-  result = eutils.run_eGquery(hash)      # working?
-  p result
-
-  puts "### run_eInfo - listing of the databases"
-  hash = {"db" => "protein"}
-  result = eutils.run_eInfo(hash)
-  p result
-
-  puts "### run_eSpell"
-  hash = {"db" => "pubmed", "term" => "kinas"}
-  result = eutils.run_eSpell(hash)
-  p result
-  p result["CorrectedQuery"]
-  
-  puts "### run_eLink"
-  hash = {"db" => "protein", "id" => "37776955"}
-  result = eutils.run_eLink(hash)        #  working?
-  p result
-
-  puts "### run_eSearch"
-  hash = {"db" => "pubmed", "term" => "kinase"}
-  result = eutils.run_eSearch(hash)
-  p result
-
-  puts "### run_eSummary"
-  hash = {"db" => "protein", "id" => "37776955"}
-  result = eutils.run_eSummary(hash)
-  p result
-
-end
-
-
-