jandot-bio 1.2.1

data/lib/bio/appl/probcons.rb

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+#
+# = bio/appl/probcons.rb - ProbCons application wrapper class
+#
+# Copyright:: Copyright (C) 2006-2007
+#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
+#             Naohisa Goto <ng@bioruby.org>
+# License::   The Ruby License
+#
+#  $Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
+#
+# Bio::Probcons is a wrapper class to execute ProbCons
+# (Probabilistic Consistency-based Multiple Alignment
+# of Amino Acid Sequences).
+#
+# == References
+# 
+# * http://probcons.stanford.edu/
+# * Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
+#   ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment.
+#   Genome Research 15: 330-340, 2005.
+#
+
+
+module Bio
+
+  # Bio::Probcons is a wrapper class to execute PROBCONS
+  # (Probabilistic Consistency-based Multiple Alignment
+  # of Amino Acid Sequences).
+  #
+  # Please refer documents in bio/apple/probcons.rb for references.
+  class Probcons < Bio::Alignment::FactoryTemplate::FileInStdoutOut
+
+    # default program name
+    DEFAULT_PROGRAM = 'probcons'.freeze
+
+    # default report parser
+    DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
+
+  end #class Probcons
+
+end #module Bio

data/lib/bio/appl/psort.rb

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+module Bio
+
+#
+# = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
+#
+# Copyright::   Copyright (C) 2003-2006
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: psort.rb,v 1.13 2007/04/05 23:35:39 trevor Exp $
+#
+
+require 'bio/appl/psort/report'
+autoload :FastaFormat, 'bio/db/fasta'
+autoload :Command, 'bio/command'
+require 'cgi'
+require 'uri'
+
+  # == 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
+  #
+  # == References
+  #
+  # * http://psort.hgc.jp/
+  #
+  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     
+    ServerURI = {
+      :IMSUT   => {
+        :PSORT1 => URI.parse("http://psort.hgc.jp/cgi-bin/okumura.pl"),
+        :PSORT2 => URI.parse("http://psort.hgc.jp/cgi-bin/runpsort.pl") },
+      :Okazaki => {
+        :PSORT1 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/okumura.pl"),
+        :PSORT2 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/runpsort.pl") },
+      :Peking  => {
+        :PSORT1 => URI.parse("http:///src.pku.edu.cn:8088/cgi-bin/okumura.pl"),
+        :PSORT2 => URI.parse("http://src.pku.edu.cn:8088/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 name and cgi path or uri.
+      #
+      # == Examples
+      #
+      #   CGIDriver.new("localhost", "/cgi-bin/psort_www.pl")
+      #
+      #   CGIDriver.new("http://localhost/cgi-bin/psort_www.pl")
+      #
+      #   CGIDriver.new(URI.parse("http://localhost/cgi-bin/psort_www.pl"))
+      #
+      def initialize(host = '', path = '')
+        case host.to_s
+        when /^http:/
+          uri = host.to_s
+        else
+          uri = 'http://' + host + '/' + path
+        end
+        @uri = URI.parse(uri)
+        @args = {}
+        @report = ''
+      end
+
+
+      # Executes a CGI ``query'' and returns aReport
+      def exec(query)
+        data = make_args(query)  
+
+        begin
+          result = nil
+          Bio::Command.start_http(@uri.host) {|http|
+            result, = http.post(@uri.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 the psort cgi script.
+      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(ServerURI[: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(ServerURI[: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(ServerURI[:Peking][:PSORT1]))
+      end
+
+
+      # Sets a cgi client (Bio::PSORT::PSORT1::Remote).
+      #
+      def initialize(driver, origin = 'yeast', title = 'MYSEQ')
+        @serv = driver
+        @origin = origin  # Gram-positive bacterium, Gram-negative bacterium,
+                          # yeast, aminal, plant
+        @title = title
+        @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 = nil, title = 'MYSEQ', origin = 'yeast')
+          @title   = title
+          @origin  = origin
+          @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 = nil)
+        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(ServerURI[:IMSUT][:PSORT2])
+      end
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
+      # connecting to the NIBB server.
+      def self.okazaki
+        self.remote(ServerURI[:Okazaki][:PSORT2])
+      end
+
+      # Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
+      # connecting to the Peking server.
+      def self.peking
+        self.remote(ServerURI[: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