bio 0.7.0

data/lib/bio/io/dbget.rb

@@ -0,0 +1,212 @@
+#
+# = bio/io/dbget.rb - GenomeNet/DBGET client module
+#
+# Copyright::	Copyright (C) 2000, 2001
+#		Mitsuteru C. Nakao <n@bioruby.org>,
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: dbget.rb,v 1.11 2005/11/05 08:32:26 k Exp $
+#
+# == DBGET
+#
+# Accessing the GenomeNet/DBGET data retrieval system
+# http://www.genome.jp/dbget/ within the intranet.
+#
+#--
+#
+#  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
+#
+#++
+#
+
+require 'socket'
+
+module Bio
+
+class DBGET
+
+  # default DBGET server address
+# SERV = "dbgetserv.genome.jp"
+  SERV = "dbget.genome.jp"
+  # default DBGET port number
+  PORT = "3266"
+
+  # Main class method to access DBGET server.  Optionally, this method
+  # can be called with the alternative DBGET server address and the
+  # TCP/IP port number.
+  #
+  # 'com' should be one of the following DBGET commands:
+  #
+  # * alink, bfind, bget, binfo, blink, bman, bref, btab, btit
+  #
+  # These methods are shortcut for the dbget commands.  Actually,
+  # Bio::DBGET.((|com|))(arg) internally calls Bio::DBGET.dbget(com, arg).
+  # Most of these methods accept the argument "-h" for help.
+  #
+  # 'arg' should be one of the following formats :
+  #
+  # * [options] db
+  #   * specify the database name only for binfo, bman etc.
+  # * [options] db:entry
+  #   * specify the database name and the entry name to retrieve.
+  # * [options] db entry1 entry2 ...
+  #   * specify the database name and the list of entries to retrieve.
+  #
+  # Note that options in the above example can be omitted.  If 'arg' is
+  # empty, the help message with a list of options for 'com' will be
+  # shown by default.  Supported database names will be found at the
+  # GenomeNet DBGET web page http://www.genome.jp/dbget/.
+  #
+  def DBGET.dbget(com, arg, serv = nil, port = nil)
+
+    unless serv or port		# if both of serv and port are nil
+      if ENV["DBGET"] =~ /:/		# and ENV["DBGET"] exists
+        serv, port = ENV["DBGET"].split(':')
+      end
+    end
+    serv = serv ? serv : SERV
+    port = port ? port : PORT
+
+    if arg.empty?
+      arg = "-h"			# DBGET help message
+    end
+
+    query = "#{com} #{arg}\n"		# DBGET query string
+
+    sock = TCPSocket.open("#{serv}", "#{port}")
+
+    sock.write(query)			# submit query
+    sock.flush			# buffer flush
+
+    sock.gets				# skip "+Helo DBgetServ ..."
+    sock.gets				# skip "#If you see this message, ..."
+    sock.gets				# skip "*Request-IDent"
+
+    result = sock.read		# DBGET result
+
+    sock.close
+
+    return result
+  end
+
+  # Show the version information of the DBGET server.
+  def DBGET.version
+    dbget("bget", "-V")
+  end
+
+
+  #--
+  # bacc("db entry")	- not supported : get accession(s)
+  # bent("db entry")	- not supported : get entry name
+  # lmarge("db entry")	- not supported
+  #++
+
+  # alink("db entry") method returns relations
+  def DBGET.alink(arg)
+    dbget("alink", arg)
+  end
+
+  # bfind("db keyword")	method searches entries by keyword
+  def DBGET.bfind(arg)
+    dbget("bfind", arg)
+  end
+
+  # bget("db entry") method retrieves entries specified by the entry names
+  def DBGET.bget(arg)
+    dbget("bget", arg)
+  end
+
+  # seq("db entry") method retrieves the first sequence of the entry
+  #
+  # Shortcut to retrieve the sequence of the entry in FASTA format.
+  # This method is equivalent to Bio::DBGET.bget("-f -n 1 #{arg}") and
+  # 'arg' should be the "db:entry" or "db entry1 entry2 ..." format.
+  def DBGET.seq(arg)
+    dbget("bget", "-f -n 1 #{arg}")
+  end
+
+  # seq2("db entry") method retrieves the second sequence of the entry if any
+  #
+  # Shortcut to retrieve the second sequence of the entry in FASTA format.
+  # This method is equivalent to Bio::DBGET.bget("-f -n 2 #{arg}").
+  # Only useful when treating the KEGG GENES database entries which have
+  # both AASEQ and NTSEQ fields. This method is obsolete and it is
+  # recommended to use 'naseq' and 'aaseq' instead.
+  def DBGET.seq2(arg)
+    dbget("bget", "-f -n 2 #{arg}")
+  end
+
+  # naseq("db entry") method retrieves the nucleic acid sequence of the
+  # entry if any.
+  def DBGET.naseq(arg)
+    dbget("bget", "-f -n n #{arg}")
+  end
+
+  # aaseq("db entry") method retrieves the amino acid sequence of the
+  # entry if any.
+  def DBGET.aaseq(arg)
+    dbget("bget", "-f -n a #{arg}")
+  end
+
+  # binfo("db")	method retrieves the database information
+  def DBGET.binfo(arg)
+    dbget("binfo", arg)
+  end
+
+  # blink("db entry") method retrieves the link information
+  def DBGET.blink(arg)
+    dbget("blink", arg)
+  end
+
+  # bman ("db entry") method shows the manual page
+  def DBGET.bman(arg)
+    dbget("bman", arg)
+  end
+
+  # bref("db entry") method retrieves the references and authors
+  def DBGET.bref(arg)
+    dbget("bref", arg)
+  end
+
+  # btab ("db entry") method retrives (and generates) the database alias table
+  def DBGET.btab(arg)
+    dbget("btab", arg)
+  end
+
+  # btit("db entry ..")	method retrieves the entry definition
+  def DBGET.btit(arg)
+    dbget("btit", arg)
+  end
+
+end
+
+end # module Bio
+
+
+if __FILE__ == $0
+  puts "### DBGET version"
+  p Bio::DBGET.version
+  puts "### DBGET.dbget('bfind', 'sce tyrosin kinase')"
+  puts Bio::DBGET.dbget('bfind', 'sce tyrosin kinase')
+  puts "### DBGET.bfind('sce tyrosin kinase')"
+  puts Bio::DBGET.bfind('sce tyrosin kinase')
+  puts "### DBGET.bget('sce:YDL028C')"
+  puts Bio::DBGET.bget('sce:YDL028C')
+  puts "### DBGET.binfo('dbget')"
+  puts Bio::DBGET.binfo('dbget')
+end
+
+

data/lib/bio/io/ddbjxml.rb

@@ -0,0 +1,614 @@
+#
+# = bio/io/ddbjxml.rb - DDBJ SOAP server access class
+#
+# Copyright::	Copyright (C) 2003, 2004
+#		KATAYAMA Toshiaki <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: ddbjxml.rb,v 1.9 2005/11/26 09:37:11 nakao Exp $
+#
+#--
+#
+#  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
+#
+#++
+#
+
+require 'bio/io/soapwsdl'
+require 'bio/db/genbank/ddbj'
+
+
+module Bio
+class DDBJ
+
+
+# = Bio::DDBJ::XML
+#
+# Accessing the DDBJ web services at
+#
+# * http://xml.nig.ac.jp/
+# * http://xml.nig.ac.jp/wsdl/index.jsp
+#
+class XML < Bio::SOAPWSDL
+
+  BASE_URI = "http://xml.nig.ac.jp/wsdl/"
+
+  # = Blast
+  #
+  # BLAST Database Search
+  #
+  # * http://xml.nig.ac.jp/doc/Blast.txt
+  #
+  # == Examples
+  #
+  #  serv = Bio::DDBJ::XML::Blast.new
+  #  query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
+  #  
+  #  report = serv.searchSimple('blastp', 'SWISS', query)
+  #  Bio::Blast::Default::Report.new(report).each_hit do |hit|
+  #    hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
+  #      p [hsps.evalue, hsps.identity, hsps.definition]
+  #    end
+  #  end
+  #
+  #  puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
+  # 
+  # == WSDL Methods
+  # 
+  # * searchSimple(program, database, query)
+  # Returns a blast report in the default format.
+  # * searchParam(program, database, query, param)
+  # Blasts with param and returns a blast report.
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/Blast.txt
+  #
+  class Blast < XML
+    SERVER_URI = BASE_URI + "Blast.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # == ClustalW
+  # 
+  # Multiple seaquece alignment using ClustalW.
+  #
+  # * http://xml.nig.ac.jp/doc/ClustalW.txt
+  #
+  # == Examples
+  #
+  #   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 serv.analyzeSimple(query)
+  #   puts serv.analyzeParam(query, '-align -matrix=blosum')
+  #
+  # == WSDL Methods
+  #
+  # * analyzeSimple(query)
+  # * analyzeParam(query, param)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/ClustalW.txt
+  #
+  class ClustalW < XML
+    SERVER_URI = BASE_URI + "ClustalW.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # = DDBJ
+  #
+  # Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
+  #
+  # * http://xml.nig.ac.jp/doc/DDBJ.txt
+  #
+  # == Examples
+  #
+  #   serv = Bio::DDBJ::XML::DDBJ.new
+  #   puts serv.getFFEntry('AB000050')
+  #   puts serv.getXMLEntry('AB000050')
+  #   puts serv.getFeatureInfo('AB000050', 'cds')
+  #   puts serv.getAllFeatures('AB000050')
+  #   puts serv.getRelatedFeatures('AL121903', '59000', '64000')
+  #   puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
+  #
+  # == WSDL Methods 
+  #
+  # * getFFEntry(accession)
+  # * getXMLEntry(accession)
+  # * getFeatureInfo(accession, feature)
+  # * getAllFeatures(accession)
+  # * getRelatedFeatures(accession, start, stop)
+  # * getRelatedFeaturesSeq(accession, start, stop)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/DDBJ.txt
+  #
+  class DDBJ < XML
+    SERVER_URI = BASE_URI + "DDBJ.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # = Fasta
+  # 
+  # Searching database using the Fasta package.
+  #
+  # * http://xml.nig.ac.jp/doc/Fasta.txt
+  # 
+  # == Examples
+  #
+  #   serv = Bio::DDBJ::XML::Fasta.new
+  #   query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
+  #    
+  #   puts serv.searchSimple('fasta34', 'PDB', query)
+  #   query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
+  #   puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
+  #
+  # == WSDL Methods
+  #
+  # * searchSimple(program, database, query)
+  # * searchParam(program, database, query, param)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/Fasta.txt
+  #
+  class Fasta < XML
+    SERVER_URI = BASE_URI + "Fasta.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # = GetEntry
+  #
+  # Retrieves database entries.
+  #
+  # * http://xml.nig.ac.jp/doc/GetEntry.txt
+  #
+  # == Examples
+  #
+  #  serv = Bio::DDBJ::XML::GetEntry.new
+  #  puts serv.getDDBJEntry('AB000050')
+  #  puts serv. getPDBEntry('1AAR')
+  #
+  # == WSDL Methods
+  #
+  # * getEntry(database, var, param1, param2)
+  # * getEntry(database, var)
+  # * getDDBJEntry(accession)
+  # * getDDBJCONEntry(accession)
+  # * getDDBJVerEntry(accession)
+  # * getLocus_DDBJEntry(locus)
+  # * getGene_DDBJEntry(gene)
+  # * getProd_DDBJEntry(products)
+  # * getPID_DDBJEntry(pid)
+  # * getClone_DDBJEntry(clone)
+  # * getXML_DDBJEntry(accession)
+  # * getEMBLEntry(accession)
+  # * getSWISSEntry(accession)
+  # * getPIREntry(accession)
+  # * getPRFEntry(accession)
+  # * getPDBEntry(accession)
+  # * getQVEntry(accession)
+  # * getDADEntry(accession)
+  # * getPID_DADEntry(pid)
+  # * getFASTA_DDBJEntry(accession)
+  # * getFASTA_DDBJCONEntry(accession)
+  # * getFASTA_DDBJVerEntry(accession)
+  # * getFASTA_DDBJSeqEntry(accession, start, end)
+  # * getFASTA_DADEntry(accession)
+  # * getFASTA_PIREntry(accession)
+  # * getFASTA_SWISSEntry(accession)
+  # * getFASTA_PDBEntry(accession)
+  # * getFASTA_PRFEntry(accession)
+  # * getFASTA_CDSEntry(accession)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/GetEntry.txt
+  #
+  class GetEntry < XML
+    SERVER_URI = BASE_URI + "GetEntry.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # = Gib
+  # 
+  # Genome Information broker
+  #
+  # * http://xml.nig.ac.jp/doc/Gib.txt
+  #
+  # == Examples
+  #
+  #   serv = Bio::DDBJ::XML::Gib.new
+  #   puts serv.getOrganismList
+  #   puts serv.getChIDList
+  #   puts serv.getOrganismNameFromChid('Sent_CT18:')
+  #   puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
+  #   puts serv.getAccession('Ecol_K12_MG1655:')
+  #   puts serv.getPieceNumber('Mgen_G37:')
+  #   puts serv.getDivision('Mgen_G37:')
+  #   puts serv.getType('Mgen_G37:')
+  #   puts serv.getCDS('Aaeo_VF5:ece1')
+  #   puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
+  #   puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
+  #
+  # == WSDL Methods
+  #
+  # * getOrganismList
+  # * getChIDList
+  # * getOrganismNameFromChid(chid)
+  # * getChIDFromOrganismName(orgName)
+  # * getAccession(chid)
+  # * getPieceNumber(chid)
+  # * getDivision(chid)
+  # * getType(chid)
+  # * getFlatFile(chid)
+  # * getFastaFile(chid, type)
+  # * getCDS(chid)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/Gib.txt
+  #
+  class Gib < XML
+    SERVER_URI = BASE_URI + "Gib.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+  
+  # = Gtop
+  #
+  # GTOP: Gene to protein.
+  #
+  # * http://xml.nig.ac.jp/doc/Gtop.txt
+  #
+  # == Examples
+  #
+  # serv = Bio::DDBJ::XML::Gtop.new
+  # puts serv.getOrganismList
+  # puts serv.getMasterInfo('thrA', 'ecol0')
+  #
+  # == WSDL Methods
+  #
+  # * getOrganismList
+  # * getMasterInfo(orfID, organism)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/Gtop.txt
+  #
+  class Gtop < XML
+    SERVER_URI = BASE_URI + "Gtop.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # == PML
+  #
+  # Variation database
+  #
+  # * http://xml.nig.ac.jp/doc/PML.txt
+  # 
+  # == Examples
+  #
+  #  serv = Bio::DDBJ::XML::PML.new
+  #  puts serv.getVariation('1')
+  #
+  # == WSDL Methods
+  #
+  # * searchVariation(field, query, order)
+  # * searchVariationSimple(field, query)
+  # * searchFrequency(field, query, order)
+  # * searchFrequencySimple(field, query)
+  # * getVariation(variation_id)
+  # * getFrequency(variation_id, population_id)
+  #
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/PML.txt
+  #
+  class PML < XML
+    SERVER_URI = BASE_URI + "PML.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+
+  # = SRS
+  #
+  # Sequence Retrieving System
+  # 
+  # * http://xml.nig.ac.jp/doc/SRS.txt
+  # 
+  # == Examples
+  #
+  #  serv = Bio::DDBJ::XML::SRS.new
+  #  puts serv.searchSimple('[pathway-des:sugar]')
+  #  puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
+  #
+  # == WSDL Methods
+  #
+  # * searchSimple(query)
+  # * searchParam(query, param)
+  #
+  # == Examples
+  #
+  # * http://xml.nig.ac.jp/doc/SRS.txt
+  #
+  class SRS < XML
+    SERVER_URI = BASE_URI + "SRS.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+  
+
+  # = TxSearch
+  #
+  # Searching taxonomy information.
+  # 
+  # * http://xml.nig.ac.jp/doc/TxSearch.txt
+  #
+  # == Examples
+  #
+  #  serv = Bio::DDBJ::XML::TxSearch.new
+  #  puts serv.searchSimple('*coli')
+  #  puts serv.searchSimple('*tardigrada*')
+  #  puts serv.getTxId('Escherichia coli')
+  #  puts serv.getTxName('562')
+  #
+  #  query = ["Campylobacter coli", "Escherichia coli"].join("\n")
+  #  rank = ["family", "genus"].join("\n")
+  #  puts serv.searchLineage(query, rank, 'Bacteria')
+  #
+  # == WSDL Methdos
+  #
+  # * searchSimple(tx_Name)
+  # * searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
+  # * getTxId(tx_Name)
+  # * getTxName(tx_Id)
+  # * searchLineage(query, ranks, superkingdom)
+  # 
+  # == References
+  #
+  # * http://xml.nig.ac.jp/doc/TxSearch.txt
+  #
+  class TxSearch < XML
+    SERVER_URI = BASE_URI + "TxSearch.wsdl"
+    def initialize(wsdl = nil)
+      super(wsdl || SERVER_URI)
+    end
+  end
+
+end # XML
+
+end # DDBJ
+end # 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
+