bio 1.4.3.0001 → 1.5.0

data/lib/bio/io/soapwsdl.rb

@@ -1,119 +0,0 @@
-#
-# = bio/io/soapwsdl.rb - SOAP/WSDL interface class
-#
-# Copyright::   Copyright (C) 2004 
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: soapwsdl.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
-#
-begin
-  require 'soap/wsdlDriver'
-rescue LoadError
-end
-
-module Bio
-
-# == Examples
-# 
-# class API < Bio::SOAPWSDL
-#   def initialize
-#     @wsdl = 'http://example.com/example.wsdl'
-#     @log = File.new("soap_log", 'w')
-#     create_driver
-#   end
-# end
-#
-# == Use HTTP proxy
-#
-# You need to set following two environmental variables
-# (case might be insensitive) as required by SOAP4R.
-#
-# --- soap_use_proxy
-#
-# Set the value of this variable to 'on'.
-#
-# --- http_proxy
-#
-# Set the URL of your proxy server (http://myproxy.com:8080 etc.).
-#
-# === Example to use HTTP proxy
-# 
-# % export soap_use_proxy=on
-# % export http_proxy=http://localhost:8080
-#
-class SOAPWSDL
-
-  # Returns URL of the current WSDL file.
-  attr_reader :wsdl
-
-  # Returns current logging IO.
-  attr_reader :log
-
-
-  def initialize(wsdl = nil)
-    @wsdl = wsdl
-    @log = nil
-    create_driver
-  end
-
-
-  def create_driver
-    if RUBY_VERSION > "1.8.2"
-      @driver = SOAP::WSDLDriverFactory.new(@wsdl).create_rpc_driver
-    else
-      @driver = SOAP::WSDLDriverFactory.new(@wsdl).create_driver
-    end
-    @driver.generate_explicit_type = true	# Ruby obj <-> SOAP obj
-  end
-  private :create_driver
-
-
-  # Change the URL for WSDL file
-  #
-  #   serv = Bio::SOAPWSDL.new("http://soap.genome.jp/KEGG.wsdl")
-  #
-  # or
-  # 
-  #   serv = Bio::SOAPWSDL.new
-  #   serv.wsdl = "http://soap.genome.jp/KEGG.wsdl"
-  #
-  # Note that you can't read two or more different WSDL files at once.
-  # In that case, create Bio::SOAPWSDL object for each.
-  #
-  def wsdl=(url)
-    @wsdl = url
-    create_driver
-  end
-
-
-  # Change the IO for logging.  The argument is passed to wiredump_dev method
-  # of the SOAP4R, thus
-  #
-  #   serv = Bio::SOAPWSDL.new
-  #   serv.log = STDERR
-  #
-  # will print all the SOAP transactions in standard error.
-  # This feature is especially useful for debug.
-  #
-  def log=(io)
-    @log = io
-    @driver.wiredump_dev = @log
-  end
-
-
-  # List of methods defined by WSDL
-  def list_methods
-    @driver.methods(false)
-  end
-
-
-  def method_missing(*arg)
-    @driver.send(*arg)
-  end
-  private :method_missing
-
-end # SOAPWSDL
-
-end # Bio
-

data/lib/bio/shell/plugin/keggapi.rb

@@ -1,181 +0,0 @@
-#
-# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
-#
-# Copyright::   Copyright (C) 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: keggapi.rb,v 1.12 2007/04/05 23:35:41 trevor Exp $
-#
-
-module Bio::Shell
-
-  module Private
-
-    module_function
-
-    def keggapi_definition2tab(list)
-      ary = []
-      list.each do |entry|
-        ary << "#{entry.entry_id}\t#{entry.definition}"
-      end
-      return ary
-    end
-  end
-
-  private
-
-  def keggapi(wsdl = nil)
-    if wsdl
-      @keggapi = Bio::KEGG::API.new(wsdl)
-    else
-      @keggapi ||= Bio::KEGG::API.new
-    end
-    return @keggapi
-  end
-
-  # DBGET
-
-  def binfo(db = "all")
-    result = keggapi.binfo(db)
-    puts result
-    return result
-  end
-
-  def bfind(str)
-    result = keggapi.bfind(str)
-    return result
-  end
-
-  def bget(str)
-    result = keggapi.bget(str)
-    if block_given?
-      yield result
-    else
-      puts result
-      return result
-    end
-  end
-
-  def btit(str)
-    result = keggapi.btit(str)
-    puts result
-    return result
-  end
-
-  def bconv(str)
-    result = keggapi.bconv(str)
-    puts result
-    return result
-  end
-
-  # DATABASES
-
-  def keggdbs
-    list = keggapi.list_databases
-    result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
-    puts result
-    return list.map {|x| x.entry_id}
-  end
-
-  def keggorgs
-    list = keggapi.list_organisms
-    result = Bio::Shell::Private.keggapi_definition2tab(list).sort.join("\n")
-    puts result
-    return list.map {|x| x.entry_id}
-  end
-
-  def keggpathways(org = "map")
-    list = keggapi.list_pathways(org)
-    result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
-    puts result
-    return list.map {|x| x.entry_id}
-  end
-
-  # use KEGG DAS insetad
-  def kegggenomeseq(org)
-    result = ""
-    require 'net/ftp'
-    Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
-      path = "/pub/kegg/genomes/#{org}"
-      list = ftp.nlst(path)
-      file = list.grep(/.*genome$/).shift
-      if file
-        open("ftp://ftp.genome.jp/#{file}") do |file|
-          result = file.read
-        end
-      end
-    end
-    return result
-  end
-
-end
-
-=begin
-
-== BioRuby extensions
-
---- get_all_best_best_neighbors_by_gene(genes_id)
---- get_all_best_neighbors_by_gene(genes_id)
---- get_all_reverse_best_neighbors_by_gene(genes_id)
---- get_all_paralogs_by_gene(genes_id)
---- get_all_genes_by_motifs(motif_id_list)
---- get_all_oc_members_by_gene(genes_id)
---- get_all_pc_members_by_gene(genes_id)
---- get_all_genes_by_organism(org)
---- get_all_linkdb_by_entry(entry_id, db)
---- save_image(url, filename = nil)
---- get_entries(ary = [])
---- get_aaseqs(ary = [])
---- get_naseqs(ary = [])
---- get_definitions(ary = [])
-
-== Original KEGG API methods
-
---- 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

data/lib/bio/shell/plugin/soap.rb

@@ -1,87 +0,0 @@
-#
-# = bio/shell/plugin/soap.rb - web services
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
-#
-# $Id: soap.rb,v 1.1 2007/07/09 11:17:09 k Exp $
-#
-
-module Bio::Shell
-
-  private
-
-  def ncbisoap(wsdl = nil)
-    if wsdl
-      @ncbisoap = Bio::NCBI::SOAP.new(wsdl)
-    else
-      @ncbisoap ||= Bio::NCBI::SOAP.new
-    end
-    return @ncbisoap
-  end
-
-  def ebisoap(wsdl = nil)
-    case wsdl
-    when :ipscan
-      @ebisoap = Bio::EBI::SOAP::InterProScan.new(wsdl)
-    when :emboss
-      @ebisoap = Bio::EBI::SOAP::Emboss.new(wsdl)
-    when :clustalw
-      @ebisoap = Bio::EBI::SOAP::ClustalW.new(wsdl)
-    when :tcoffee
-      @ebisoap = Bio::EBI::SOAP::TCoffee.new(wsdl)
-    when :muscle
-      @ebisoap = Bio::EBI::SOAP::Muscle.new(wsdl)
-    when :fasta
-      @ebisoap = Bio::EBI::SOAP::Fasta.new(wsdl)
-    when :wublast
-      @ebisoap = Bio::EBI::SOAP::WUBlast.new(wsdl)
-    when :mpsrch
-      @ebisoap = Bio::EBI::SOAP::MPsrch.new(wsdl)
-    when :scanps
-      @ebisoap = Bio::EBI::SOAP::ScanPS.new(wsdl)
-    when :msd
-      @ebisoap = Bio::EBI::SOAP::MSD.new(wsdl)
-    when :ontology
-      @ebisoap = Bio::EBI::SOAP::Ontology.new(wsdl)
-    when :citation
-      @ebisoap = Bio::EBI::SOAP::Citation.new(wsdl)
-    when /^http/
-      @ebisoap = Bio::EBI::SOAP.new(wsdl)
-    else
-      @ebisoap ||= Bio::EBI::SOAP.new
-    end
-    return @ebisoap
-  end
-
-  def ddbjsoap(wsdl = nil)
-    case wsdl
-    when :blast
-      @ddbjsoap = Bio::DDBJ::XML::Blast.new
-    when :fasta
-      @ddbjsoap = Bio::DDBJ::XML::Fasta.new
-    when :clustalw
-      @ddbjsoap = Bio::DDBJ::XML::ClustalW.new
-    when :ddbj
-      @ddbjsoap = Bio::DDBJ::XML::DDBJ.new
-    when :gib
-      @ddbjsoap = Bio::DDBJ::XML::Gib.new
-    when :gtop
-      @ddbjsoap = Bio::DDBJ::XML::Gtop.new
-    when :pml
-      @ddbjsoap = Bio::DDBJ::XML::PML.new
-    when :srs
-      @ddbjsoap = Bio::DDBJ::XML::SRS.new
-    when :txsearch
-      @ddbjsoap = Bio::DDBJ::XML::TxSearch.new
-    when /^http/
-      @ddbjsoap = Bio::DDBJ::XML.new(wsdl)
-    else
-      @ddbjsoap ||= Bio::DDBJ::XML.new
-    end
-    return @ddbjsoap
-  end
-
-end
-

data/sample/dbget

@@ -1,37 +0,0 @@
-#!/usr/bin/env ruby
-#
-# dbget - DBGET client
-#
-#  Interface to GenomeNet DBGET system - http://www.genome.jp/dbget/
-#
-#   Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation; either version 2 of the License, or
-#  (at your option) any later version.
-#
-#  This program 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 General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-#
-#  $Id: dbget,v 1.7 2004/08/24 00:09:24 k Exp $
-#
-
-require "bio/io/dbget"
-
-# DBGET command
-com = File.basename($0)			# e.g. $PATH/bget db entry
-com = ARGV.shift if com == "dbget"	# e.g. $PATH/dbget bget db entry
-
-# DBGET query strings
-arg = ARGV.join(" ")
-
-# DBGET result
-print Bio::DBGET.dbget(com, arg)
-

data/sample/demo_ddbjxml.rb

@@ -1,212 +0,0 @@
-#
-# = sample/demo_ddbjxml.rb - demonstration of Bio::DDBJ::XML, DDBJ SOAP access
-#
-# Copyright::	Copyright (C) 2003, 2004
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	The Ruby License
-#
-#
-#
-# == Description
-#
-# Demonstration of Bio::DDBJ::XML, DDBJ SOAP server access class.
-#
-# == Requirements
-#
-# Internet connection is needed.
-#
-# == Usage
-#
-# Simply run this script.
-#
-#  $ ruby demo_ddbjxml.rb
-#
-# == Notes
-#
-# It can not be run with Ruby 1.9 because SOAP4R (SOAP support for Ruby)
-# currently does not support Ruby 1.9.
-#
-# == Development information
-#
-# The code was moved from lib/bio/io/ddbjxml.rb.
-#
-
-require 'bio'
-
-#if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  puts ">>> Bio::DDBJ::XML::Blast"
-  serv = Bio::DDBJ::XML::Blast.new
-# serv.log = STDERR
-
-  query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
-
-  puts "### searchSimple('blastp', 'SWISS', query)"
-  puts serv.searchSimple('blastp', 'SWISS', query)
-
-  puts "### searchParam('tblastn', 'ddbjvrl', query, '-m 8')"
-  puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
-
-
-  puts ">>> Bio::DDBJ::XML::ClustalW"
-  serv = Bio::DDBJ::XML::ClustalW.new
-
-  query = <<END
-> RABSTOUT   rabbit Guinness receptor
-   LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
-   ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
-> MUSNOSE   mouse nose drying factor
-    mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
-    fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
-> HSHEAVEN    human Guinness receptor repeat
- mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
- fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
- mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
- fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
-END
-
-  puts "### analyzeSimple(query)"
-  puts serv.analyzeSimple(query)
-
-  puts "### analyzeParam(query, '-align -matrix=blosum')"
-  puts serv.analyzeParam(query, '-align -matrix=blosum')
-
-
-  puts ">>> Bio::DDBJ::XML::DDBJ"
-  serv = Bio::DDBJ::XML::DDBJ.new
-
-  puts "### getFFEntry('AB000050')"
-  puts serv.getFFEntry('AB000050')
-
-  puts "### getXMLEntry('AB000050')"
-  puts serv.getXMLEntry('AB000050')
-
-  puts "### getFeatureInfo('AB000050', 'cds')"
-  puts serv.getFeatureInfo('AB000050', 'cds')
-
-  puts "### getAllFeatures('AB000050')"
-  puts serv.getAllFeatures('AB000050')
-
-  puts "### getRelatedFeatures('AL121903', '59000', '64000')"
-  puts serv.getRelatedFeatures('AL121903', '59000', '64000')
-
-  puts "### getRelatedFeaturesSeq('AL121903', '59000', '64000')"
-  puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
-
-
-  puts ">>> Bio::DDBJ::XML::Fasta"
-  serv = Bio::DDBJ::XML::Fasta.new
-
-  query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
-
-  puts "### searchSimple('fasta34', 'PDB', query)"
-  puts serv.searchSimple('fasta34', 'PDB', query)
-
-  query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
-
-  puts "### searchParam('fastx34_t', 'PDB', query, '-n')"
-  puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
-
-
-  puts ">>> Bio::DDBJ::XML::GetEntry"
-  serv = Bio::DDBJ::XML::GetEntry.new
-
-  puts "### getDDBJEntry('AB000050')"
-  puts serv.getDDBJEntry('AB000050')
-
-  puts "### getPDBEntry('1AAR')"
-  puts serv. getPDBEntry('1AAR')
-
-
-  puts ">>> Bio::DDBJ::XML::Gib"
-  serv = Bio::DDBJ::XML::Gib.new
-
-  puts "### getOrganismList"
-  puts serv.getOrganismList
-
-  puts "### getChIDList"
-  puts serv.getChIDList
-
-  puts "### getOrganismNameFromChid('Sent_CT18:')"
-  puts serv.getOrganismNameFromChid('Sent_CT18:')
-
-  puts "### getChIDFromOrganismName('Aquifex aeolicus VF5')"
-  puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
-
-  puts "### getAccession('Ecol_K12_MG1655:')"
-  puts serv.getAccession('Ecol_K12_MG1655:')
-
-  puts "### getPieceNumber('Mgen_G37:')"
-  puts serv.getPieceNumber('Mgen_G37:')
-
-  puts "### getDivision('Mgen_G37:')"
-  puts serv.getDivision('Mgen_G37:')
-
-  puts "### getType('Mgen_G37:')"
-  puts serv.getType('Mgen_G37:')
-
-  puts "### getCDS('Aaeo_VF5:ece1')"
-  puts serv.getCDS('Aaeo_VF5:ece1')
-
-  puts "### getFlatFile('Nost_PCC7120:pCC7120zeta')"
-  puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
-
-  puts "### getFastaFile('Nost_PCC7120:pCC7120zeta')"
-  puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
-
-
-  puts ">>> Bio::DDBJ::XML::Gtop"
-  serv = Bio::DDBJ::XML::Gtop.new
-
-  puts "### getOrganismList"
-  puts serv.getOrganismList
-
-  puts "### getMasterInfo"
-  puts serv.getMasterInfo('thrA', 'ecol0')
-
-
-#  puts ">>> Bio::DDBJ::XML::PML"
-#  serv = Bio::DDBJ::XML::PML.new
-#
-#  puts "### getVariation('1')"
-#  puts serv.getVariation('1')
-
-
-  puts ">>> Bio::DDBJ::XML::SRS"
-  serv = Bio::DDBJ::XML::SRS.new
-
-  puts "### searchSimple('[pathway-des:sugar]')"
-  puts serv.searchSimple('[pathway-des:sugar]')
-
-  puts "### searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')"
-  puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
-
-
-  puts ">>> Bio::DDBJ::XML::TxSearch"
-  serv = Bio::DDBJ::XML::TxSearch.new
-
-  puts "### searchSimple('*coli')"
-  puts serv.searchSimple('*coli')
-
-  puts "### searchSimple('*tardigrada*')"
-  puts serv.searchSimple('*tardigrada*')
-
-  puts "### getTxId('Escherichia coli')"
-  puts serv.getTxId('Escherichia coli')
-
-  puts "### getTxName('562')"
-  puts serv.getTxName('562')
-
-  query = "Campylobacter coli\nEscherichia coli"
-  rank = "family\ngenus"
-
-  puts "### searchLineage(query, rank, 'Bacteria')"
-  puts serv.searchLineage(query, rank, 'Bacteria')
-
-#end