bio 1.0.0 → 1.1.0

data/lib/bio/appl/probcons.rb

@@ -0,0 +1,41 @@
+#
+# = 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

@@ -1,79 +1,57 @@
+module Bio
+
 #
 # = 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
+# Copyright::   Copyright (C) 2003-2006
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#
-#--
-#
-#  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: psort.rb,v 1.13 2007/04/05 23:35:39 trevor Exp $
 #
 
-require 'bio/sequence'
-require 'bio/db/fasta'
-require 'net/http'
+require 'bio/appl/psort/report'
+autoload :FastaFormat, 'bio/db/fasta'
+autoload :Command, 'bio/command'
 require 'cgi'
-
-
-module Bio
-
-  
-
-
+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     
-    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'}
+    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 
@@ -103,12 +81,26 @@ module Bio
       attr_reader :report
 
 
-      # Sets remote ``host'' and cgi ``path''.
-      def initialize(host = '', path = '') 
-        @host = host
-        @path = path
+      # 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
+        @report = ''
       end
 
 
@@ -117,7 +109,10 @@ module Bio
         data = make_args(query)  
 
         begin
-          result, = Net::HTTP.new(@host).post(@path, data)
+          result = nil
+          Bio::Command.start_http(@uri.host) {|http|
+            result, = http.post(@uri.path, data)
+          }
           @report = result.body
           output = parse_report(@report)
         end
@@ -139,7 +134,7 @@ module Bio
 
       # Erases HTML tags
       def erase_html_tags(str)
-        return str.gsub(/<\S.*?>/,'')
+        return str.gsub(/<\S.*?>/, '')
       end
 
       # Returns CGI argument text in String (key=value&) from a Hash ({key=>value}).
@@ -148,7 +143,7 @@ module Bio
         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
+        return tmp.join(delim)  # not ';' but '&' in the psort cgi script.
       end
 
     end # class CGIDriver
@@ -156,6 +151,7 @@ module Bio
 
 
     # = Bio::PSORT::PSORT1
+    #
     # Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
     #
     # == Example
@@ -168,9 +164,11 @@ module Bio
     #  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'
@@ -178,33 +176,31 @@ module Bio
       # 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']))
+        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(WWWServer['Okazaki']['host'],
-                            WWWServer['Okazaki']['PSORT1']))
+        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(WWWServer['Peking']['host'],
-                            WWWServer['Peking']['PSORT1']))
+        self.new(Remote.new(ServerURI[: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'
+      # 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
 
@@ -236,9 +232,9 @@ module Bio
       # 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}
+          @title = faa.entry_id if @title == 'MYSEQ'
+          @sequence = faa.seq
+          @serv.args = {'title' => @title, 'origin' => @origin}
           @serv.parsing = parsing
           return @serv.exec(sequence)
         else
@@ -267,9 +263,9 @@ module Bio
         attr_accessor :parsing
         
         # Sets remote ``host'' and cgi ``path''.
-        def initialize(host, path)
-          @origin  = 'yeast'
-          @title   = 'MYSEQ'
+        def initialize(host, path = nil, title = 'MYSEQ', origin = 'yeast')
+          @title   = title
+          @origin  = origin
           @parsing = true
           super(host, path)
         end
@@ -326,29 +322,26 @@ module Bio
       #  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)
+      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(WWWServer['IMSUT']['host'],
-                    WWWServer['IMSUT']['PSORT2'])
+        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(WWWServer['Okazaki']['host'],
-                    WWWServer['Okazaki']['PSORT2'])
+        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(WWWServer['Peking']['host'],
-                    WWWServer['Peking']['PSORT2'])
+        self.remote(ServerURI[:Peking][:PSORT2])
       end
 
       # An accessor of the origin argument.
@@ -373,9 +366,9 @@ module Bio
       # 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}
+          @title = faa.entry_id if @title == nil
+          @sequence = faa.seq
+          @serv.args = {'origin' => @origin, 'title' => @title}
           @serv.parsing = parsing
           return @serv.exec(@sequence)
         else

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

@@ -1,38 +1,22 @@
 #
 # = bio/appl/psort/report.rb - PSORT systems report classes
 #
-# Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
-# License::     LGPL
+# Copyright::   Copyright (C) 2003 
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  $Id: report.rb,v 1.12 2005/11/03 10:50:58 nakao Exp $
+#  $Id: report.rb,v 1.15 2007/04/05 23:35:40 trevor Exp $
 #
 # == A Report classes for PSORT Systems
 # 
-#--
-#
-#  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/appl/psort'
 
 
 module Bio
 
+  autoload :Sequence, 'bio/sequence'
+
   class PSORT
 
     class PSORT1

data/lib/bio/appl/pts1.rb

@@ -0,0 +1,263 @@
+module Bio
+
+#
+# = bio/appl/pts1.rb - A web service client of PTS1, predicting for the 
+#   peroxisomal targeting signal type 1.
+#
+# Copyright::   Copyright (C) 2006 
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: pts1.rb,v 1.5 2007/04/05 23:35:39 trevor Exp $
+#
+
+require 'uri'
+require 'net/http'
+require 'bio/db/fasta'
+require 'bio/command'
+
+# = Bio::PTS1 - A web service client class for PTS1 predictor.
+#
+# == Peroxisomal targeting signal type 1 (PTS1) predictor
+#
+# Bio::PTS1 class is a client of the PTS1 predictor.
+#
+# == Examples
+#
+#   require 'bio'
+#   sp = Bio::SPTR.new(Bio::Fetch.query("sp", "p53_human"))
+#   faa = sp.seq.to_fasta(sp.entry_id)
+#   pts1 = Bio::PTS1.new
+#   report = pts1.exec_remote(faa)
+#   report.output     #=> "<HTML>\n<HEAD><TITLE>PTS1 Prediction Server ..."
+#   report.prediction #=> "Not targeted"
+#   report.cterm      #=> "KLMFKTEGPDSD"
+#   report.score      #=> "-79.881"
+#   report.fp         #=> "67.79%"
+#   report.sppta      #=> "-1.110"
+#   report.spptna     #=> "-41.937"
+#   report.profile    #=> "-36.834"
+#
+# == References
+#
+# * The PTS1 predictor
+#   http://mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp
+#
+# * Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. 
+#   Motif refinement of the peroxisomal targeting signal 1 and evaluation 
+#   of taxon-specific differences. 
+#   J Mol Biol. 2003 May 2;328(3):567-79. PMID: 12706717 
+#
+# * Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. 
+#   Prediction of peroxisomal targeting signal 1 containing proteins from 
+#   amino acid sequence. 
+#   J Mol Biol. 2003 May 2;328(3):581-92. PMID: 12706718 
+#
+class PTS1
+
+  # Organism specific parameter value: function names.
+  FUNCTION = {
+    'METAZOA-specific' => 1,
+    'FUNGI-specific'   => 2,
+    'GENERAL'          => 3,
+  }
+
+  # Output report.
+  attr_reader :output
+
+  # Used function name (Integer). 
+  # function_name = Bio::PTS1::FUNCTION.find_all {|k,v| v == pts1.function }[0][0]
+  attr_reader :function
+
+  # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['METAZOA-specific'])
+  def self.new_with_metazoa_function
+    self.new('METAZOA-specific')
+  end
+
+  # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['FUNGI-specific'])
+  def self.new_with_fungi_function
+    self.new('FUNGI-specific')
+  end
+
+  # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['GENERAL'])
+  def self.new_with_general_function
+    self.new('GENERAL')
+  end
+
+   
+  # Constructs Bio::PTS1 web service client.
+  # 
+  # == Examples
+  #
+  #   serv_default_metazoa_specific = Bio::PTS1.new
+  #   serv_general_function = Bio::PTS1.new('GENERAL')
+  #   serv_fungi_specific = Bio::PTS1.new(2)    # See Bio::PTS1::FUNCTION.
+  #
+  def initialize(func = 'METAZOA-specific')
+    @host = "mendel.imp.ac.at"
+    @cgi_path = "/sat/pts1/cgi-bin/pts1.cgi"
+    @output = nil
+    @function = function(func)
+  end
+
+
+  # Sets and shows the function parameter.
+  #
+  # Organism specific parameter: function names (Bio::PTS1::FUNTION.keys).
+  #
+  #
+  # == Examples
+  #
+  #  # sets function name parameter.
+  #  serv = Bio::PTS1.new
+  #  serv.function('METAZOA-specific')
+  #
+  #  # shows function name parameter.
+  #  serv.function #=> "METAZOA-specific"
+  # 
+  def function(func = nil)
+    return @function.keys.to_s if func == nil
+
+    if FUNCTION.values.include?(func)
+      @function = Hash[*FUNCTION.find {|x| x[1] == func}]
+    elsif FUNCTION[func]
+      @function = {func => FUNCTION[func]} 
+    else
+      raise ArgumentError, 
+            "Invalid argument: #{func}", 
+            "Available function names: #{FUNCTION.keys.inspect}"
+    end
+    @function
+  end
+
+
+  # Executes the query request and returns result output in Bio::PTS1::Report.
+  # The query argument is available both aSting in fasta format text and 
+  # aBio::FastaFormat.
+  #
+  # == Examples
+  # 
+  #   require 'bio'
+  #   pts1 = Bio::PTS1.new
+  #   pts1.exec(">title\nKLMFKTEGPDSD")
+  #
+  #   pts1.exec(Bio::FastaFormat.new(">title\nKLMFKTEGPDSD"))
+  #
+  def exec(query)
+    seq = set_sequence_in_fastaformat(query)
+    
+    @form_data = {'function' => @function.values.to_s,
+                  'sequence' => seq.seq,
+                  'name'     => seq.definition }
+    @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
+
+    result, = Bio::Command.post_form(@uri, @form_data)
+    @output = Report.new(result.body)
+    
+    return @output
+  end
+
+  private 
+
+  # Sets query sequence in Fasta Format if any.
+  def set_sequence_in_fastaformat(query)
+    if query.class == Bio::FastaFormat
+      return query
+    else
+      return Bio::FastaFormat.new(query)
+    end
+  end
+
+
+  # = Parser for the PTS1 prediction Report (in HTML).
+  #
+  #
+  class Report
+
+    # Query sequence name.
+    attr_reader :entry_id
+
+    # Amino acids subsequence at C-terminal region.
+    attr_reader :cterm
+
+    # Score
+    attr_reader :score
+
+    # Profile
+    attr_reader :profile
+
+    # S_ppt (non accessibility)
+    attr_reader :spptna
+
+    # S_ppt (accessibility)
+    attr_reader :sppta
+
+    # False positive probability
+    attr_reader :fp
+
+    # Prediction ("Targeted", "Twilight zone" and "Not targeted")
+    attr_reader :prediction
+    
+    # Raw output
+    attr_reader :output
+
+    # Parsing PTS1 HTML report.
+    # 
+    # == Example
+    #
+    #   report = Bio::PTS1::Report.new(str)
+    #   report.cterm 
+    #
+    def initialize(str)
+      @cterm   = ''
+      @score   = 0
+      @profile = 0
+      @spptna  = 0
+      @sppta   = 0
+      @fp      = 0
+      @prediction = 0
+      
+      if /PTS1 query prediction/m =~ str
+        @output = str
+        parse
+      else
+        raise 
+      end
+    end
+
+
+    private
+
+    def parse
+      @output.each do |line|
+        case line
+        when /Name<\/td><td>(\S.+)<\/td><\/tr>/
+          @entry_id = $1
+        when /C-terminus<\/td><td>(\w+)<\/td>/
+          @cterm = $1
+        when /Score<\/b><td><b>(-?\d.+?)<\/b><\/td><\/tr>/
+          @score = $1
+        when /Profile<\/i><\/td><td>(.+?)<\/td>/
+          @profile = $1
+        when /S_ppt \(non-accessibility\)<\/i><\/td><td>(.+?)<\/td>/
+          @spptna = $1
+        when /S_ppt \(accessibility\)<\/i><\/td><td>(.+?)<\/td>/
+          @sppta = $1
+        when /P\(false positive\)<\/i><\/td><td>(.+?)<\/td>/
+          @fp = $1
+        when /Prediction classification<\/i><\/td><td>(\w.+?)<\/td>/
+          @prediction = $1
+        else
+        end
+      end
+    end
+    
+  end # class Report
+  
+end # class PTS1
+
+end # module Bio
+
+
+
+