jandot-bio 1.2.1

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

@@ -0,0 +1,267 @@
+#
+# = bio/appl/targetp/report.rb - TargetP report class
+# 
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: report.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
+#
+# == Description
+#
+# TargetP class for http://www.cbs.dtu.dk/services/TargetP/
+#
+# == Example
+# == References
+#
+
+module Bio
+
+
+  class TargetP
+
+    # = A parser and container class for TargetP report.
+    class Report
+
+      # Delimiter
+      DELIMITER = "\n \n"
+
+      # Delimiter      
+      RS = DELIMITER
+
+      # Returns the program version.
+      attr_reader :version
+      
+      # Returns the query sequences.
+      attr_reader :query_sequences
+
+      # Returns 'included' or 'not included'.
+      # If the value is 'included', Bio::TargetP::Report#prediction['TPlen']
+      # contains a valid value.
+      attr_reader :cleavage_site_prediction
+      
+      # Returns ``PLANT'' or ``NON-PLANT'' networks.
+      attr_reader :networks
+
+      # Returns a Hash of the prediction results.
+      #
+      # {"Name"=>"MGI_2141503", "Loc."=>"_", "RC"=>3, "SP"=>0.271,
+      #  "other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
+      # 
+      # Keys: Name, Len, SP, mTP, other, Loc, RC
+      # Optional key for PLANT networks: cTP
+      # Optional key in Cleavage site: TPlen
+      #
+      # Use 'Length' and 'Loc.' instead of 'Len' and 'Loc' respectively
+      # for the version 1.0 report.
+      attr_reader :prediction
+
+      # Returns a Hash of cutoff values.
+      attr_reader :cutoff
+
+      # Sets output report.
+      def initialize(str)
+        @version                  = nil
+        @query_sequences          = nil
+        @cleavage_site_prediction = nil
+        @networks                 = nil
+        @prediction               = {}
+        @cutoff                   = {}
+        parse_entry(str)
+      end
+
+      alias pred prediction
+
+      # Returns the name of query sequence.
+      def name
+        @prediction['Name']
+      end
+      alias entry_id name 
+
+      # Returns length of query sequence.
+      def query_len
+        if @prediction['Len']
+          @prediction['Len']
+        else
+          @prediction['Length']
+        end
+      end
+      alias length query_len
+
+      # Returns the predicted localization signal: 
+      # 1. S (Signal peptide)
+      # 2. M (mTP)
+      # 3. C (cTP)
+      # 4. * 
+      # 5. _
+      def loc
+        if @prediction['Loc'] 
+          @prediction['Loc']   # version 1.0
+        else
+          @prediction['Loc.']  # version 1.1
+        end
+      end
+
+      # Returns RC.
+      def rc
+        @prediction['RC']
+      end
+      
+      private
+
+      # 
+      def parse_entry(str)
+        labels = []
+        cutoff = []
+        values = []
+
+        str.split("\n").each {|line|
+          case line
+          when /targetp v(\d+.\d+)/,/T A R G E T P\s+(\d+.\d+)/
+            @version = $1
+
+          when /Number of (query|input) sequences:\s+(\d+)/
+            @query_sequences = $1.to_i
+
+          when /Cleavage site predictions (\w.+)\./ 
+            @cleavage_site_prediction = $1
+
+          when /Using (\w+.+) networks/
+            @networks = $1
+          when /Name +Len/
+            labels = line.sub(/^\#\s*/,'').split(/\s+/)
+
+          when /cutoff/
+            cutoff = line.split(/\s+/)
+            cutoff.shift
+            labels[2, 4].each_with_index {|loc, i|
+              next if loc =~ /Loc/
+              @cutoff[loc] = cutoff[i].to_f
+            }
+          when /-----$/
+          when /^ +$/, ''
+          else
+            values = line.sub(/^\s*/,'').split(/\s+/)
+            values.each_with_index {|val, i|
+              label = labels[i]
+              case label
+              when 'RC', /Len/ 
+                val = val.to_i
+              when 'SP','mTP','cTP','other'
+                val = val.to_f
+              end
+              @prediction[label] = val
+            }
+          end
+        }
+      end
+
+    end # class Report
+    
+  end # class TargetP
+
+end # moudel Bio
+
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp 
+  rescue LoadError
+  end
+
+
+  plant = <<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions not included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+HOGE
+
+plant_c = <<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC     TPlen
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3	  -
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+
+HOGE
+
+non_plant_c = <<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using NON-PLANT networks.
+ 
+#                        Name   Length    mTP   SP  other  Loc.  RC   TPlen
+#--------------------------------------------------------------------------
+                     MGI_96083	 2187	0.292 0.053 0.746   _     3	  -
+#--------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00
+
+
+
+HOGE
+
+
+  def hoge(e)
+    puts e
+    ent = Bio::TargetP::Report.new(e)
+    pp ent
+
+    p [:entry_id, ent.entry_id]
+    p [:name, ent.name]
+    p [:version, ent.version]
+    p [:query_sequnces, ent.query_sequences]
+    p [:cleavage_site_prediction, ent.cleavage_site_prediction]
+    p [:networks, ent.networks]
+    p [:query_len, ent.query_len]
+    p [:prediction, ent.prediction]
+    p [:pred_Name, ent.pred['Name']]
+    p [:pred_SP, ent.pred['SP']]
+    p [:pred_mTP, ent.pred['mTP']]
+    p [:cutoff, ent.cutoff]
+    p [:loc, ent.loc]
+    p [:rc, ent.rc]
+
+    puts '=='
+  end
+
+
+  [plant, plant_c, non_plant_c].each {|e|
+    hoge(e)
+  }
+
+  exit  if ARGV.size == 0
+
+  while ent = $<.gets(Bio::TargetP::Report::DELIMITER)
+    hoge(ent)
+  end
+
+end
+
+
+

data/lib/bio/appl/tcoffee.rb

@@ -0,0 +1,55 @@
+#
+# = bio/appl/tcoffee.rb - T-Coffee 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: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
+#
+# Bio::Tcoffee is a wrapper class to execute T-Coffee.
+#
+# == References
+#
+# * http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+# * Notredame, C., Higgins, D.G. and Heringa, J.
+#   T-Coffee: A novel method for fast and accurate multiple sequence
+#   alignment. J. Mol. Biol. 302: 205-217, 2000.
+#
+
+
+module Bio
+
+  # Bio::Tcoffee is a wrapper class to execute t-coffee.
+  #
+  # Please refer documents in bio/apple/tcoffee.rb for references.
+  class Tcoffee < Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
+
+    # default program name
+    DEFAULT_PROGRAM = 't_coffee'.freeze
+
+    # default report parser
+    DEFAULT_PARSER = Bio::ClustalW::Report
+
+    private
+    # generates options specifying input filename.
+    # returns an array of string
+    def _option_input_file(fn)
+      [ '-infile', fn ]
+    end
+
+    # generates options specifying output filename.
+    # returns an array of string
+    def _option_output_file(fn)
+      [ '-outfile', fn ]
+    end
+
+    # generates options specifying output filename.
+    # returns an array of string
+    def _option_output_dndfile(fn)
+      [ '-newtree', fn ]
+    end
+  end #class TCoffee
+
+end #module Bio

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

@@ -0,0 +1,222 @@
+#
+# = bio/appl/tmhmm/report.rb - TMHMM report class
+# 
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: report.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
+#
+# == Description
+#
+#
+# == Example
+# == References
+#
+
+module Bio
+
+  # = TMHMM class for http://www.cbs.dtu.dk/services/TMHMM/
+  class TMHMM
+
+    # Splits multiple reports into a report entry.
+    def TMHMM.reports(data)
+      entry     = []
+      ent_state = ''
+      data.each_line do |line|
+        if /^\#/ =~ line
+          if ent_state == 'next'
+            ent_state = 'entry'
+          elsif ent_state == 'tmh'
+            ent_state = 'next'
+          end
+        else
+          ent_state = 'tmh'
+        end
+
+        if ent_state != 'next'
+          entry << line
+        else
+          if block_given?
+            yield Bio::TMHMM::Report.new(entry)
+          else
+            Bio::TMHMM::Report.new(entry)
+          end
+          entry = [line]
+        end
+      end
+
+      if block_given?
+        yield Bio::TMHMM::Report.new(entry)
+      else
+        Bio::TMHMM::Report.new(entry)
+      end
+    end
+
+    # = TMHMM report parser class.
+    class Report
+
+      # Returns an Array of Bio::TMHMM::TMH.
+      attr_reader :tmhs
+
+      # Returns
+      attr_reader :entry_id
+
+      # Returns
+      attr_reader :query_len
+
+      # Returns
+      attr_reader :predicted_tmhs
+
+      # Returns
+      attr_reader :exp_aas_in_tmhs
+
+      # Returns
+      attr_reader :exp_first_60aa
+
+      # Returns
+      attr_reader :total_prob_of_N_in
+
+      alias length query_len
+
+      #
+      def initialize(entry = nil)
+        parse_header(entry)
+        @tmhs = parse_tmhs(entry)
+      end
+
+      # Returns an Array of Bio::TMHMM::TMH including only "TMhelix".
+      def helix
+        @tmhs.map {|t| t if t.status == 'TMhelix' }.compact
+      end
+
+      #
+      def to_s
+        [
+          [
+            ["Length:",                    @query_len],
+            ["Number of predicted TMHs:",  @predicted_tmhs],
+            ["Exp number of AAs in THMs:", @exp_aas_in_tmhs],
+            ["Exp number, first 60 AAs:",  @exp_first_60aa],
+            ["Total prob of N-in:",        @total_prob_of_N_in]
+          ].map {|e| "\# " + [@entry_id, e].flatten.join("\t") },
+          tmhs.map {|ent| ent.to_s }
+        ].flatten.join("\n")
+      end
+
+
+      private
+
+      #
+      def parse_header(raw)
+        raw.each do |line|
+          next unless /^#/.match(line)
+
+          case line
+          when / (\S.+) Length: +(\d+)/
+            @entry_id  = $1.strip
+            @query_len = $2.to_i
+          when /Number of predicted TMHs: +(\d+)/
+            @predicted_tmhs  = $1.to_i
+          when /Exp number of AAs in TMHs: +([\d\.]+)/
+            @exp_aas_in_tmhs = $1.to_f
+          when /Exp number, first 60 AAs: +([\d\.]+)/
+            @exp_first_60aa  = $1.to_f
+          when /Total prob of N-in: +([\d\.]+)/
+            @total_prob_of_N_in = $1.to_f
+          end
+        end
+      end
+
+      #
+      def parse_tmhs(raw)
+        tmhs = []
+        raw.each do |line|
+          case line
+          when /^[^\#]/
+            eid,version,status,r0,r1 = line.split(/\s+/)
+            tmhs << Bio::TMHMM::TMH.new(eid.strip,
+                                        version.strip, 
+                                        status.strip, 
+                                        Range.new(r0.to_i, r1.to_i))
+          end
+        end
+        tmhs
+      end
+
+    end # class Report
+
+
+    # = Container class of the trainsmembrane helix(TMH) and the other
+    #   segments.
+    class TMH
+
+      # Returns
+      attr_accessor :entry_id
+
+      # Returns
+      attr_accessor :version
+
+      # Returns the status of the TMH. ("outside", "TMhelix" or "inside").
+      attr_accessor :status
+
+      # Returns an Range of TMH position.
+      attr_accessor :range
+
+      alias pos range
+
+      #
+      def initialize(entry_id = nil, version = nil, status = nil, range = nil)
+        @entry_id = entry_id
+        @version  = version
+        @status   = status
+        @range    = range
+      end
+
+      #
+      def to_s
+        [@entry_id, @version, @status, @range.first, @range.last].join("\t")
+      end
+
+    end # class TMH
+
+  end # class TMHMM
+
+end # module Bio
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  Bio::TMHMM.reports(ARGF.read) do |ent|
+    puts '==>'
+    puts ent.to_s
+    pp ent
+
+    p [:entry_id, ent.entry_id]
+    p [:query_len, ent.query_len]
+    p [:predicted_tmhs, ent.predicted_tmhs]
+    p [:tmhs_size, ent.tmhs.size]
+    p [:exp_aas_in_tmhs, ent.exp_aas_in_tmhs]
+    p [:exp_first_60aa, ent.exp_first_60aa]
+    p [:total_prob_of_N_in, ent.total_prob_of_N_in]
+
+    ent.tmhs.each do |t|
+      p t
+      p [:entry_id, t.entry_id]
+      p [:version, t.version]
+      p [:status, t.status]
+      p [:range, t.range]
+      p [:pos, t.pos]
+    end
+
+    p [:helix, ent.helix]
+    p ent.tmhs.map {|t| t if t.status == 'TMhelix' }.compact
+  end
+
+end