bio 1.4.3.0001 → 1.5.0

data/lib/bio/io/ebisoap.rb

@@ -1,158 +0,0 @@
-#
-# = bio/io/emblsoap.rb - EBI SOAP server access class
-#
-# Copyright::  Copyright (C) 2006
-#              Toshiaki Katayama <k@bioruby.org>
-# License::    The Ruby License
-#
-# $Id: ebisoap.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-
-require 'bio/io/soapwsdl'
-
-module Bio
-class EBI
-
-class SOAP < Bio::SOAPWSDL
-
-  BASE_URI = "http://www.ebi.ac.uk/Tools/webservices/wsdl/"
-
-  # set default to Dbfetch
-  SERVER_URI = BASE_URI + "WSDbfetch.wsdl"
-
-  def initialize(wsdl = nil)
-    super(wsdl || self.class::SERVER_URI)
-  end
-
-  # * fetchData
-  # * getSupportedDBs
-  # * getSupportedFormats
-  # * getSupportedStyles
-  class Dbfetch < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSDbfetch.wsdl"
-  end
-
-  # * checkStatus
-  # * doIprscan
-  # * getResults
-  # * poll
-  # * polljob
-  # * runInterProScan
-  # * test
-  class InterProScan < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSInterProScan.wsdl"
-  end
-
-  # * checkStatus
-  # * getInfo
-  # * getResults
-  # * getTools
-  # * poll
-  # * run
-  # * test
-  class Emboss < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSEmboss.wsdl"
-  end
-
-  # * checkStatus
-  # * getResults
-  # * poll
-  # * runClustalW
-  # * test
-  class ClustalW < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSClustalW.wsdl"
-  end
-
-  # * checkStatus
-  # * getResults
-  # * poll
-  # * runTCoffee
-  class TCoffee < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSTCoffee.wsdl"
-  end
-
-  # * checkStatus
-  # * getResults
-  # * poll
-  # * runMuscle
-  # * test
-  class Muscle < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSMuscle.wsdl"
-  end
-
-  # * checkStatus
-  # * doFasta
-  # * getResults
-  # * poll
-  # * polljob
-  # * runFasta
-  class Fasta < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSFasta.wsdl"
-  end
-
-  # * checkStatus
-  # * doWUBlast
-  # * getIds
-  # * getResults
-  # * poll
-  # * polljob
-  # * runWUBlast
-  # * test
-  class WUBlast < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSWUBlast.wsdl"
-  end
-
-  # * checkStatus
-  # * getResults
-  # * poll
-  # * runMPsrch
-  # * test
-  class MPsrch < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSMPsrch.wsdl"
-  end
-
-  # * checkStatus
-  # * getResults
-  # * poll
-  # * runScanPS
-  # * test
-  class ScanPS < Bio::EBI::SOAP
-    SERVER_URI = BASE_URI + "WSScanPS.wsdl"
-  end
-
-  class MSD < Bio::EBI::SOAP
-    SERVER_URI = "http://www.ebi.ac.uk/msd-srv/docs/api/msd_soap_service.wsdl"
-  end
-
-  class Ontology < Bio::EBI::SOAP
-    SERVER_URI = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl"
-  end
-
-  class Citation < Bio::EBI::SOAP
-    SERVER_URI = "http://www.ebi.ac.uk/citations/webservices/wsdl"
-  end
-
-end # SOAP
-
-end # EBI
-end # Bio
-
-
-
-if __FILE__ == $0
-  serv = Bio::EBI::SOAP::Dbfetch.new
-  p serv.getSupportedDBs
-
-  require 'base64'
-
-  serv = Bio::EBI::SOAP::Emboss.new
-  hash = {"tool" => "water",
-          "asequence" => "uniprot:alk1_human",
-          "bsequence" => "uniprot:alk1_mouse",
-          "email" => "ebisoap@example.org"}
-  poll = serv.run(hash, [])
-  puts poll
-  base = serv.poll(poll, "tooloutput")
-  puts Base64.decode64(base)  
-end
-

data/lib/bio/io/ensembl.rb

@@ -1,229 +0,0 @@
-#
-# = bio/io/ensembl.rb - An Ensembl Genome Browser client.
-#
-# Copyright::   Copyright (C) 2006
-#               Mitsuteru C. Nakao <n@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-# == Description
-#
-# Client classes for Ensembl Genome Browser.
-#
-# == Examples
-#
-#  human = Bio::Ensembl.new('Homo_sapiens')
-#  seq = human.exportview(1, 1000, 100000)
-#  gff = human.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
-#
-#  human = Bio::Ensembl.human
-#  seq = human.exportview(1, 1000, 100000)
-#  gff = human.exportview(1, 1000, 100000, ['gene'])
-#
-#  seq = Bio::Ensembl.human.exportview(1, 1000, 100000)
-#  gff = Bio::Ensembl.human.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
-#
-#  
-# == References
-#
-# * Ensembl
-#   http:/www.ensembl.org/
-#
-
-require 'bio/command'
-
-module Bio
-
-# == Description
-#
-# An Ensembl Genome Browser client class.
-#
-# == Examples
-#
-#  human = Bio::Ensembl.new('Homo_sapiens')
-#  seq = human.exportview(1, 1000, 100000)
-#  gff = human.exportview(1, 1000, 100000, ['gene'])
-#
-#  mouse = Bio::Ensembl.new('Mus_musculus')
-#  seq = mouse.exportview(1, 1000, 100000)
-#  gff = mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
-#
-#  rice = Bio::Enesmbl.new('Oryza_sativa', 'http://www.gramene.org')
-#  seq = rice.exportview(1, 1000, 100000)
-#
-# == References
-#
-# * Ensembl
-#   http:/www.ensembl.org/
-#
-# * GRAMENE
-#   http://www.gramene.org/
-#
-class Ensembl
-  
-  ENSEMBL_URL = 'http://www.ensembl.org'
-
-  # Server URL (ex. 'http://www.ensembl.org')
-  attr_reader :server
-
-  # Organism name. (ex. 'Homo_sapiens').
-  attr_reader :organism
-
-  def initialize(organism, server = nil)
-    @server = server || ENSEMBL_URL
-    @organism = organism
-    @uri = [ @server.chomp('/'), @organism ].join('/')
-  end
-
-  def self.human
-    self.new("Homo_sapiens")
-  end
-
-  def self.mouse
-    self.new("Mus_musculus")
-  end
-
-  # Ensembl ExportView Client.
-  #
-  # Retrieve genomic sequence/features from Ensembl ExportView in plain text.
-  # Ensembl ExportView exports genomic data (sequence and features) in 
-  # several file formats including fasta, GFF and tab.
-  #
-  # * ExportViwe (http://www.ensembl.org/Homo_sapiens/exportview).
-  #
-  # == Examples
-  #
-  #   human = Bio::Ensembl.new('Homo_sapiens')
-  #     or
-  #   human = Bio::Ensembl.human
-  #
-  #   # Genomic sequence in Fasta format
-  #   human.exportview(:seq_region_name => 1, 
-  #                    :anchor1 => 1149206, :anchor2 => 1149229)
-  #   human.exportview(1, 1149206, 1149229)
-  #
-  #   # Feature in GFF
-  #   human.exportview(:seq_region_name => 1, 
-  #                    :anchor1 => 1149206, :anchor2 => 1150000, 
-  #                    :options => ['similarity', 'repeat', 
-  #                                 'genscan', 'variation', 'gene'])
-  #   human.exportview(1, 1149206, 1150000, ['variation', 'gene'])
-  #   
-  # Feature in TAB
-  #   human.exportview(:seq_region_name => 1, 
-  #                    :anchor1 => 1149206, :anchor2 => 1150000, 
-  #                    :options => ['similarity', 'repeat', 
-  #                                 'genscan', 'variation', 'gene'],
-  #                    :format => 'tab')
-  #
-  # == Arguments
-  #
-  # Bio::Ensembl#exportview method allow both orderd arguments and 
-  # named arguments. (Note: mandatory arguments are marked by '*').
-  #
-  # === Orderd Arguments
-  #
-  # 1. seq_region_name - Chromosome number (*)
-  # 2. anchor1         - From coordination (*)
-  # 3. anchor2         - To coordination (*)
-  # 4. options         - Features to export (in :format => 'gff' or 'tab')
-  #                      ['similarity', 'repeat', 'genscan', 'variation', 
-  #                       'gene']
-  #
-  # === Named Arguments
-  # 
-  # * :seq_region_name - Chromosome number (*)
-  # * :anchor1         - From coordination (*)
-  # * :anchor2         - To coordination (*)
-  # * :type1           - From coordination type ['bp', ]
-  # * :type2           - To coordination type ['bp', ]
-  # * :upstream        - Bp upstream
-  # * :downstream      - Bp downstream
-  # * :format          - File format ['fasta', 'gff', 'tab']
-  # * :options         - Features to export (for :format => 'gff' or 'tab')
-  #                      ['similarity', 'repeat', 'genscan', 'variation', 
-  #                       'gene']
-  # 
-  def exportview(*args)
-    defaults = {
-      :type1 => 'bp', 
-      :type2 => 'bp', 
-      :downstream => '', 
-      :upstream => '', 
-      :format => 'fasta',
-      :options => [],
-      :action => 'export', 
-      :_format => 'Text', 
-      :output => 'txt', 
-      :submit => 'Continue >>'
-    }
-
-    if args.first.class == Hash
-      options = args.first
-      if options[:options] and options[:format] != 'fasta' and options[:format] != 'tab' 
-        options.update({:format => 'gff'}) 
-      end
-    else
-      options = {
-        :seq_region_name => args[0], 
-        :anchor1 => args[1], 
-        :anchor2 => args[2],
-      }
-
-      case args[3]
-      when Array
-        options.update({:format => 'gff', :options => args[3]}) 
-      when Hash
-        options.update(args[3])
-      end
-
-      if args[4].class == Hash
-        options.update(args[4])
-      end
-    end
-
-    params = defaults.update(options)
-
-    result = Bio::Command.post_form("#{@uri}/exportview", params)
-
-    return result.body
-  end
-
-end # class Ensembl
-
-end # module Bio
-
-
-
-# Codes for backward-compatibility.
-#
-class Bio::Ensembl
-  EBIServerURI = ENSEMBL_URL
-
-  def self.server_uri(uri = nil)
-    if uri
-      @uri = uri
-    else
-      @uri || EBIServerURI
-    end
-  end
-    
-  class Base
-    def self.exportview(*args)
-      Bio::Ensembl.new(Organism).exportview(*args)
-    end
-  end
-  
-  class Human < Base
-    Organism = Bio::Ensembl.human.organism
-  end
-  
-  class Mouse < Base
-    Organism = Bio::Ensembl.mouse.organism
-  end
-end # class Bio::Ensembl
-
-
-
-

data/lib/bio/io/higet.rb

@@ -1,73 +0,0 @@
-#
-# = bio/io/higet.rb - SOAP interface for HGC HiGet
-#
-# Copyright::  Copyright (C) 2005 Toshiaki Katayama <k@bioruby.org>
-#
-# $Id: higet.rb,v 1.3 2006/09/19 05:46:22 k Exp $
-#
-
-require 'bio/io/soapwsdl'
-
-module Bio
-class HGC
-
-# == Description
-#
-# Interface for the HiGet service provided by Human Genome Center (HGC), Japan.
-# HiGet performs full-text search against various biological databases.
-#
-# == References
-#
-# * http://higet.hgc.jp/
-#
-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
-