bio 0.7.0

data/lib/bio/appl/mafft.rb

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+#
+# = bio/appl/mafft.rb - MAFFT wrapper class
+#
+# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+# License::   LGPL
+#
+#--
+#  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: mafft.rb,v 1.9 2005/12/18 15:58:40 k Exp $
+#
+# Bio::MAFFT is a wrapper class to execute MAFFT.
+# MAFFT is a very fast multiple sequence alignment software.
+#
+# = Important Notes
+#
+# Though Bio::MAFFT class currently supports only MAFFT version 3,
+# you can use MAFFT version 5 because the class is a wrapper class.
+#
+# == References
+#
+# * K. Katoh, K. Misawa, K. Kuma and T. Miyata.
+#   MAFFT: a novel method for rapid multiple sequence alignment based
+#   on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066, 2002.
+#   http://nar.oupjournals.org/cgi/content/abstract/30/14/3059
+# * http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
+#
+
+require 'bio/db/fasta'
+require 'bio/io/flatfile'
+
+#--
+# We use Open3.popen3, because MAFFT on win32 requires Cygwin.
+#++
+require 'open3'
+
+module Bio
+
+  # Bio::MAFFT is a wrapper class to execute MAFFT.
+  # MAFFT is a very fast multiple sequence alignment software.
+  #
+  # Though Bio::MAFFT class currently supports only MAFFT version 3,
+  # you can use MAFFT version 5 because the class is a wrapper class.
+  class MAFFT
+
+    autoload :Report,       'bio/appl/mafft/report'
+
+    # Creates a new alignment factory.
+    # When +n+ is a number (1,2,3, ...), performs 'fftns n'.
+    # When +n+ is :i or 'i', performs 'fftnsi'.
+    def self.fftns(n = nil)
+      opt = []
+      if n.to_s == 'i' then
+        self.new2(nil, 'fftnsi', *opt)
+      else
+        opt << n.to_s if n
+        self.new2(nil, 'fftns', *opt)
+      end
+    end
+
+    # Creates a new alignment factory.
+    # Performs 'fftnsi'.
+    def self.fftnsi
+      self.new2(nil, 'fftnsi')
+    end
+
+    # Creates a new alignment factory.
+    # When +n+ is a number (1,2,3, ...), performs 'nwns n'.
+    # When +n+ is :i or 'i', performs 'nwnsi'.
+    # In both case, if all_positive is true, add option '--all-positive'.
+    def self.nwns(n = nil, ap = nil)
+      opt = []
+      opt << '--all-positive' if ap
+      if n.to_s == 'i' then
+        self.new2(nil, 'nwnsi', *opt)
+      else
+        opt << n.to_s if n
+        self.new2(nil, 'nwns', *opt)
+      end
+    end
+
+    # Creates a new alignment factory.
+    # Performs 'nwnsi'.
+    # If +all_positive+ is true, add option '--all-positive'.
+    def self.nwnsi(all_positive = nil)
+      opt = []
+      opt << '--all-positive' if all_positive
+      self.new2(nil, 'nwnsi', *opt)
+    end
+
+    # Creates a new alignment factory.
+    # Performs 'nwns --all-positive n' or 'nwnsi --all-positive'.
+    # Same as Bio::MAFFT.nwap(n, true).
+    def self.nwap(n = nil)
+      self.nwns(n, true)
+    end
+
+    # Creates a new alignment factory.
+    # +dir+ is the path of the MAFFT program.
+    # +prog+ is the name of the program.
+    # +opt+ is options of the program.
+    def self.new2(dir, prog, *opt)
+      if dir then
+        prog = File.join(dir, prog)
+      end
+      self.new(prog, opt)
+    end
+
+    # Creates a new alignment factory.
+    # +program+ is the name of the program.
+    # +opt+ is options of the program.
+    def initialize(program, option)
+      @program = program
+      @option = option
+      @command = nil
+      @output = nil
+      @report = nil
+      @log = nil
+    end
+
+    # program name
+    attr_accessor :program
+
+    # options
+    attr_accessor :option
+
+    # Shows last command-line string. Returns nil or an array of String.
+    # Note that filenames described in the command-line may already
+    # be removed because they are temporary files.
+    attr_reader :command
+
+    # last message to STDERR when executing the program.
+    attr_reader :log
+
+    # Shows latest raw alignment result.
+    # Since a result of MAFFT is simply a multiple-fasta format,
+    # it returns an array of Bio::FastaFormat instances
+    # instead of raw string.
+    attr_reader :output
+
+    # Shows last alignment result (instance of Bio::MAFFT::Report class)
+    # performed by the factory.
+    attr_reader :report
+
+    # Executes the program.
+    # If +seqs+ is not nil, perform alignment for seqs.
+    # If +seqs+ is nil, simply executes the program.
+    def query(seqs)
+      if seqs then
+        query_align(seqs)
+      else
+        exec_local(@option)
+      end
+    end
+
+    # Performs alignment for seqs.
+    # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+    def query_align(seqs, *arg)
+      unless seqs.is_a?(Bio::Alignment)
+        seqs = Bio::Alignment.new(seqs, *arg)
+      end
+      query_string(seqs.to_fasta(70))
+    end
+
+    # Performs alignment for +str+.
+    # Str should be a string that can be recognized by the program.
+    def query_string(str, *arg)
+      begin
+        tf_in = Tempfile.open('align')
+        tf_in.print str
+      ensure
+        tf_in.close(false)
+      end
+      r = query_by_filename(tf_in.path, *arg)
+      tf_in.close(true)
+      r
+    end
+
+    # Performs alignment of sequences in the file named +fn+.
+    def query_by_filename(fn, seqtype = nil)
+      opt = @option + [ fn ]
+      exec_local(opt)
+      @report = Report.new(@output, seqtype)
+      @report
+    end
+
+    private
+    # Executes a program in the local machine.
+    def exec_local(opt)
+      @command = [ @program, *opt ]
+      #STDERR.print "DEBUG: ", @command.join(" "), "\n"
+      @output = nil
+      @log = nil
+      Open3.popen3(*@command) do |din, dout, derr|
+        din.close
+        derr.sync = true
+        t = Thread.start do
+          @log = derr.read
+        end
+        ff = Bio::FlatFile.new(Bio::FastaFormat, dout)
+        @output = ff.to_a
+        t.join
+      end
+      @log
+    end
+
+  end #class MAFFT
+end #module Bio
+

data/lib/bio/appl/mafft/report.rb

@@ -0,0 +1,119 @@
+#
+# = bio/appl/mafft/report.rb - MAFFT report class
+#
+# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+# License::   LGPL
+#
+#--
+#  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: report.rb,v 1.8 2005/12/18 15:58:40 k Exp $
+#
+# MAFFT result parser class.
+# MAFFT is a very fast multiple sequence alignment software.
+#
+# Since a result of MAFFT is simply a multiple-fasta format,
+# the significance of this class is to keep standard form and
+# interface between Bio::ClustalW::Report.
+#
+# == References
+#
+# * K. Katoh, K. Misawa, K. Kuma and T. Miyata.
+#   MAFFT: a novel method for rapid multiple sequence alignment based
+#   on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066, 2002.
+#   http://nar.oupjournals.org/cgi/content/abstract/30/14/3059
+# * http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
+#
+
+require 'bio/db/fasta'
+require 'bio/io/flatfile'
+require 'bio/appl/mafft'
+
+module Bio
+  class MAFFT
+
+    # MAFFT result parser class.
+    # MAFFT is a very fast multiple sequence alignment software.
+    #
+    # Since a result of MAFFT is simply a multiple-fasta format,
+    # the significance of this class is to keep standard form and
+    # interface between Bio::ClustalW::Report.
+    class Report
+
+      # Creates a new Report object.
+      # +ary+ should be an Array of Bio::FastaFormat.
+      # +seqclass+ should on of following:
+      # Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
+      # String: 'PROTEIN', 'DNA', ...
+      def initialize(ary, seqclass = nil)
+        @data = ary
+        @align = nil
+        case seqclass
+        when /PROTEIN/i
+          @seqclass = Bio::Sequence::AA
+        when /[DR]NA/i
+          @seqclass = Bio::Sequence::NA
+        else
+          if seqclass.is_a?(Module) then
+            @seqclass = seqclass
+          else
+            @seqclass = Bio::Sequence
+          end
+        end
+      end
+
+      # sequence data. Returns an array of Bio::FastaFormat.
+      attr_reader :data
+
+      # Sequence class (Bio::Sequence::AA, Bio::Sequence::NA, ...)
+      attr_reader :seqclass
+
+      # Gets an multiple alignment.
+      # Returns an instance of Bio::Alignment class.
+      def align
+        do_parse() unless @align
+        @align
+      end
+      alias alignment align
+
+      # Gets an fasta-format string of the sequences.
+      # Returns a string.
+      # Same as align.to_fasta.
+      # Please refer to Bio::Alignment#to_fasta for arguments.
+      def to_fasta(*arg)
+        align.to_fasta(*arg)
+      end
+
+      # Gets an array of the sequences.
+      # Returns an array of Bio::FastaFormat instances.
+      def to_a
+        @data
+      end
+
+      private
+      # Parsing a result.
+      def do_parse
+        return nil if @align
+        @align = Bio::Alignment.new(@data) do |x|
+          [ @seqclass.new(x.seq), x.definition ]
+        end
+        nil
+      end
+
+    end #class Report
+  end #class MAFFT
+end #module Bio
+

data/lib/bio/appl/psort.rb

@@ -0,0 +1,555 @@
+#
+# = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
+#
+# Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
+# License::     LGPL
+#
+#
+# $Id: psort.rb,v 1.8 2005/11/01 05:15:15 nakao Exp $
+#
+# == A client for PSORT WWW Server 
+#
+# A client for PSORT WWW Server for predicting protein subcellular 
+# localization.
+#
+# PSORT family members,
+# 1. PSORT
+# 2. PSORT II
+# 3. iPSORT
+# 4. PSORT-B  http://psort.org
+# 5. WoLF-PSORT
+#
+# See http://psort.ims.u-tokyo.ac.jp.
+#
+# === Example
+#
+#
+#--
+#
+#  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/sequence'
+require 'bio/db/fasta'
+require 'net/http'
+require 'cgi'
+
+
+module Bio
+
+  
+
+
+  class PSORT
+    # a Hash for PSORT official hosts:
+    #   Key      value (host)
+    #   -------  -----------------------
+    #   IMSUT    psort.ims.u-tokyo.ac.jp  
+    #   Okazaki  psort.nibb.ac.jp        
+    #   Peking   srs.pku.edu.cn:8088     
+    WWWServer = {
+      'IMSUT'   => {'host' => 'psort.hgc.jp', #'psort.ims.u-tokyo.ac.jp', 
+                    'PSORT1' => '/cgi-bin/okumura.pl',
+                    'PSORT2' => '/cgi-bin/runpsort.pl'},
+      'Okazaki' => {'host' => 'psort.nibb.ac.jp', 
+                    'PSORT1' => '/cgi-bin/okumura.pl',
+                    'PSORT2' => '/cgi-bin/runpsort.pl'},
+      'Peking'  => {'host' => 'srs.pku.edu.en:8088', 
+                    'PSORT1' => '/cgi-bin/okumura.pl',
+                    'PSORT2' => '/cgi-bin/runpsort.pl'}
+    }
+
+
+    # = Generic CGI client class
+    # A generic CGI client class for Bio::PSORT::* classes.
+    # The class provides an interface for CGI argument processing and output 
+    # report parsing.
+    #
+    # == Example
+    # 
+    #  class NewClient < CGIDriver
+    #    def initialize(host, path)
+    #      super(host, path)
+    #    end
+    #  end
+    #  private
+    #  def make_args(query)
+    #    # ...
+    #  end
+    #  def parse_report(output)
+    #    # ...
+    #  end
+    #
+    class CGIDriver
+
+      # CGI query argument in Hash ({key => value, ...}).
+      attr_accessor :args
+
+      # CGI output raw text
+      attr_reader :report
+
+
+      # Sets remote ``host'' and cgi ``path''.
+      def initialize(host = '', path = '') 
+        @host = host
+        @path = path
+        @args = {}
+        @report
+      end
+
+
+      # Executes a CGI ``query'' and returns aReport
+      def exec(query)
+        data = make_args(query)  
+
+        begin
+          result, = Net::HTTP.new(@host).post(@path, data)
+          @report = result.body
+          output = parse_report(@report)
+        end
+
+        return output
+      end
+
+      private
+
+      # Bio::CGIDriver#make_args. An API skelton.
+      def make_args(args_hash)
+        # The routin should be provided in the inherited class
+      end
+
+      # Bio::CGIDriver#parse_report. An API skelton.
+      def parse_report(result_body)
+        # The routin should be provided in the inherited class
+      end
+
+      # Erases HTML tags
+      def erase_html_tags(str)
+        return str.gsub(/<\S.*?>/,'')
+      end
+
+      # Returns CGI argument text in String (key=value&) from a Hash ({key=>value}).
+      def args_join(hash, delim = '&')
+        tmp = []
+        hash.each do |key, val|
+          tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
+        end
+        return tmp.join(delim)  # not ';' but '&' in psort's cgi
+      end
+
+    end # class CGIDriver
+
+
+
+    # = Bio::PSORT::PSORT1
+    # Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
+    #
+    # == Example
+    # 
+    #  serv = Bio::PSORT::PSORT1.imsut
+    #  serv.title = 'Query_title_splited_by_white space'
+    #  serv.exec(seq, false)  # seq.class => String
+    #  serv.exec(seq)
+    #  report = serv.exec(Bio::FastaFormat.new(seq))
+    #  report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
+    # 
+    # == References
+    # 1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein 
+    #    localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
+    #    [PMID:1478671]
+    class PSORT1
+
+      autoload :Report, 'bio/appl/psort/report'
+
+      # Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)     
+      # connecting to the IMSUT server.
+      def self.imsut
+        self.new(Remote.new(WWWServer['IMSUT']['host'],
+                            WWWServer['IMSUT']['PSORT1']))
+      end
+
+
+      # Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
+      # connecting to the NIBB server.
+      def self.okazaki
+        self.new(Remote.new(WWWServer['Okazaki']['host'],
+                            WWWServer['Okazaki']['PSORT1']))
+      end
+      
+
+      # Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
+      # connecting to the Peking server.
+      def self.peking
+        self.new(Remote.new(WWWServer['Peking']['host'],
+                            WWWServer['Peking']['PSORT1']))
+      end
+
+
+      # Sets a server CGI Driver (Bio::PSORT::PSORT1::Remote).
+      def initialize(driver, origin = 'yeast')
+        @serv     = driver
+        @origin   = origin  # Gram-positive bacterium, Gram-negative bacterium,
+                            # yeast, aminal, plant
+        @title    = 'MYSEQ'
+        @sequence = ''
+      end
+
+
+      # An accessor of the origin argument. Default setting is "yeast".
+      # Usable values:
+      # 1. Gram-positive bacterium
+      # 2. Gram-negative bacterium
+      # 3. yeast
+      # 4. animal
+      # 5. plant
+      attr_accessor :origin
+
+      # An accessor of the query sequence argument.
+      attr_accessor :sequence
+
+      # An accessor of the title argument. Default setting is 'MYSEQ'.
+      # The value is automatically setted if you use a query in
+      # Bio::FastaFormat.
+      attr_accessor :title
+
+
+      # Executes the query (faa) and returns an Bio::PSORT::PSORT1::Report.
+      #
+      # The ``faa'' argument is acceptable a sequence both in String and in 
+      # Bio::FastaFormat.
+      #
+      # If you set the second argument is ``parsing = false'', 
+      # returns ourput text without any parsing.
+      def exec(faa, parsing = true)
+        if faa.class == Bio::FastaFormat
+          @title        = faa.entry_id if @title == 'MYSEQ'
+          @sequence     = faa.seq
+          @serv.args    = {'title' => @title, 'origin' => @origin}
+          @serv.parsing = parsing
+          return @serv.exec(sequence)
+        else
+          self.exec(Bio::FastaFormat.new(faa), parsing)
+        end
+      end
+
+
+      # =  Bio::PSORT::PSORT1::Remote
+      # PSORT1 specific CGIDriver.
+      class Remote < CGIDriver
+
+        # Accessor for Bio::PSORT::PSORT1::Remote#origin to contein target domain.
+        # Taget domains:
+        # 1. Gram-positive bacterium
+        # 2. Gram-negative bacterium
+        # 3. yeast
+        # 4. animal
+        # 5. plant
+        attr_accessor :origin
+
+        # Accessor for Bio::POSRT::PSORT1#sequence to contein the query sequence.
+        attr_accessor :title
+
+        # Accessor for Bio::PSORT::PSORT1#title to contain the query title.
+        attr_accessor :parsing
+        
+        # Sets remote ``host'' and cgi ``path''.
+        def initialize(host, path)
+          @origin  = 'yeast'
+          @title   = 'MYSEQ'
+          @parsing = true
+          super(host, path)
+        end
+
+        private
+
+        # Returns parsed CGI argument.
+        # An API implementation.
+        def make_args(query)
+          @args.update({'sequence' => query})
+          return args_join(@args)
+        end
+
+
+        # Returns parsed output report. 
+        # An API implementation.
+        def parse_report(str)
+          str = erase_html_tags(str)
+          str = Bio::PSORT::PSORT1::Report.parser(str) if @parsing
+          return str
+        end
+
+      end # Class Remote
+
+    end # class PSORT1
+
+      
+    # = Bio::PSORT::PSORT2
+    # Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.
+    #
+    # == Example
+    # 
+    #  serv = Bio::PSORT::PSORT2.imsut
+    #  serv.title = 'Query_title_splited_by_white space'
+    #  serv.exec(seq, false)  # seq.class => String
+    #  serv.exec(seq)
+    #  report = serv.exec(Bio::FastaFormat.new(seq))
+    #  report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
+    #
+    # == References
+    # 1. Nakai, K. and Horton, P., PSORT: a program for detecting the sorting 
+    #    signals of proteins and predicting their subcellular localization, 
+    #    Trends Biochem. Sci, 24(1) 34-35 (1999).
+    #    [PMID:10087920]
+    class PSORT2
+
+      autoload :Report, 'bio/appl/psort/report'
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote).
+      #
+      # PSORT official hosts:
+      #  key      host                     path
+      #  -------  -----------------------  --------------------  ---------
+      #  IMSUT    psort.ims.u-tokyo.ac.jp  /cgi-bin/runpsort.pl  (default)
+      #  Okazaki  psort.nibb.ac.jp         /cgi-bin/runpsort.pl
+      #  Peking   srs.pku.edu.cn:8088      /cgi-bin/runpsort.pl
+      def self.remote(host, path)
+        self.new(Remote.new(host, path))
+      end
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)     
+      # connecting to the IMSUT server.
+      def self.imsut
+        self.remote(WWWServer['IMSUT']['host'],
+                    WWWServer['IMSUT']['PSORT2'])
+      end
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
+      # connecting to the NIBB server.
+      def self.okazaki
+        self.remote(WWWServer['Okazaki']['host'],
+                    WWWServer['Okazaki']['PSORT2'])
+      end
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
+      # connecting to the Peking server.
+      def self.peking
+        self.remote(WWWServer['Peking']['host'],
+                    WWWServer['Peking']['PSORT2'])
+      end
+
+      # An accessor of the origin argument.
+      # Default setting is ``yeast''.
+      attr_accessor :origin
+
+      # An accessor of the title argument. Default setting is ``QUERY''.
+      # The value is automatically setted if you use a query in
+      # Bio::FastaFormat.
+      attr_accessor :title
+
+      # Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).
+      def initialize(driver, origin = 'yeast')
+        @serv   = driver
+        @origin = origin
+        @title  = ''
+      end
+
+
+      # Executes PSORT II prediction and returns Report object 
+      # (Bio::PSORT::PSORT2::Report) if parsing = true.
+      # Returns PSORT II report in text if parsing = false.
+      def exec(faa, parsing = true)
+        if faa.class == Bio::FastaFormat
+          @title        = faa.entry_id if @title == nil
+          @sequence     = faa.seq
+          @serv.args    = {'origin' => @origin, 'title' => @title}
+          @serv.parsing = parsing
+          return @serv.exec(@sequence)
+        else
+          self.exec(Bio::FastaFormat.new(faa), parsing)
+        end
+      end
+
+
+      # = Bio::PSORT::PSORT2::Remote
+      # PSORT2 specific CGIDriver
+      class Remote < CGIDriver
+
+        # Sets remote ``host'' and cgi ``path''.
+        def initialize(host, path)
+          @origin = 'yeast'
+          super(host, path)
+          @parsing = true
+        end
+        
+        # An accessor of the origin argument.
+        # Default setting is ``yeast''.
+        attr_accessor :origin
+
+        # An accessor of the output parsing.
+        # Default setting is ``true''.
+        attr_accessor :parsing
+
+        
+        private
+         
+        # Returns parsed CGI argument.
+        # An API implementation.
+        def make_args(query)
+          @args.update({'sequence' => query})
+          return args_join(@args)
+        end
+
+
+        # Returns parsed output report. 
+        # An API implementation.
+        def parse_report(str)
+          str = str.gsub(/\n<hr>/i, Report::BOUNDARY)
+          str = erase_html_tags(str)
+          str = Bio::PSORT::PSORT2::Report.parser(str, self.args['title']) if @parsing
+          return str
+        end
+
+      end # class Remote
+
+    end # class PSORT2      
+
+
+    class IPSORT
+    end # class IPSORT
+
+    
+    class PSORTB
+    end # class PSORTB
+
+    class WoLF_PSORT
+    end # class PSORTB
+
+  end # class PSORT
+
+end # module Bio
+
+
+
+
+
+if __FILE__ == $0
+
+  begin
+    require 'psort/report.rb'
+  rescue LoadError
+  end
+
+
+  seq = ">hoge mit
+MALEPIDYTT RDEDDLDENE LLMKISNAAG SSRVNDNNDD LTFVENDKII 
+ARYSIQTSSK QQGKASTPPV EEAEEAAPQL PSRSSAAPPP PPRRATPEKK 
+DVKDLKSKFE GLAASEKEEE EMENKFAPPP KKSEPTIISP KPFSKPQEPV
+FKGYHVQVTA HSREIDAEYL KIVRGSDPDT TWLIISPNAK KEYEPESTGS 
+KKSFTPSKSP APVSKKEPVK TPSPAPAAKI PKENPWATAE YDYDAAEDNE
+NIEFVDDDWW LGELEKDGSK GLFPSNYVSL LPSRNVASGA PVQKEEPEQE 
+SFHDFLQLFD ETKVQYGLAR RKAKQNSGNA ETKAEAPKPE VPEDEPEGEP
+DDWNEPELKE RDFDQAPLKP NQSSYKPIGK IDLQKVIAEE KAKEDPRLVQ
+DYKKIGNPLP GMHIEADNEE EPEENDDDWD DDEDEAAQPP ANFAAVANNL 
+KPTAAGSKID DDKVIKGFRN EKSPAQLWAE VSPPGSDVEK IIIIGWCPDS 
+APLKTRASFA PSSDIANLKN ESKLKRDSEF NSFLGTTKPP SMTESSLKND
+KAEEAEQPKT EIAPSLPSRN SIPAPKQEEA PEQAPEEEIE GN
+"
+  Seq1 = ">hgoe
+LTFVENDKII NI
+"
+
+  puts "\n Bio::PSORT::PSORT"
+  
+  puts "\n ==> p serv = Bio::PSORT::PSORT.imsut"
+  p serv = Bio::PSORT::PSORT1.imsut
+
+  puts "\n ==> p serv.class "  
+  p serv.class
+
+  puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
+  p serv.title = 'Query_title_splited_by_white space'
+
+  puts "\n ==> p serv.exec(seq, false) "  
+  p serv.exec(seq, false)
+
+  puts "\n ==> p serv.exec(seq) "  
+  p serv.exec(seq)
+
+  puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) "  
+  p report = serv.exec(Bio::FastaFormat.new(seq))
+
+  puts "\n ==> p report.class"
+  p report.class
+
+
+  puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) "  
+  p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
+
+  puts "\n ==> p report_raw.class"
+  p report_raw.class
+
+
+  puts "\n ==> p report.methods" 
+  p report.methods
+
+  methods = ['entry_id', 'origin', 'title', 'sequence','result_info',
+             'reasoning', 'final_result', 'raw']
+  methods.each do |method|
+    puts "\n ==> p report.#{method}"
+    p eval("report.#{method}")
+  end
+
+
+
+  puts "\n Bio::PSORT::PSORT2"
+
+  puts "\n ==> p serv = Bio::PSORT::PSORT2.imsut"
+  p serv = Bio::PSORT::PSORT2.imsut
+
+  puts "\n ==> p serv.class "
+  p serv.class
+
+  puts "\n ==> p seq "
+  p seq
+
+  puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
+  p serv.title = 'Query_title_splited_by_white space'
+
+  puts "\n ==> p serv.exec(seq) # parsed report" 
+  p serv.exec(seq)
+
+  puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) # parsed report" 
+  p report = serv.exec(Bio::FastaFormat.new(seq))
+
+
+
+  puts "\n ==> p serv.exec(seq, false) # report in plain text"
+  p serv.exec(seq, false)
+
+  puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) # report in plain text"
+  p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
+
+
+  puts "\n ==> p report.methods"
+  p report.methods
+
+  methods = ['entry_id', 'scl', 'definition', 'seq', 'features', 'prob', 'pred', 'k', 'raw']
+  methods.each do |method|
+    puts "\n ==> p report.#{method}"
+    p eval("report.#{method}")
+  end
+end