bio 1.0.0 → 1.1.0

data/lib/bio/appl/fasta/format10.rb

@@ -1,268 +1,313 @@
 #
-# bio/appl/fasta/format10.rb - FASTA output (-m 10) parser
+# = bio/appl/fasta/format10.rb - FASTA output (-m 10) parser
 # 
-#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2002 Toshiaki Katayama <k@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: format10.rb,v 1.6 2005/09/26 13:00:05 k Exp $
+# $Id: format10.rb,v 1.7 2007/04/06 12:04:05 k Exp $
 #
 
 require 'bio/appl/fasta'
 
 module Bio
-  class Fasta
+class Fasta
+
+# Summarized results of the fasta execution results.
+class Report
+
+  def initialize(data)
+    # header lines - brief list of the hits
+    if data.sub!(/.*\nThe best scores are/m, '')
+      data.sub!(/(.*)\n\n>>>/m, '')
+      @list = "The best scores are" + $1
+    else
+      data.sub!(/.*\n!!\s+/m, '')
+      data.sub!(/.*/) { |x| @list = x; '' }
+    end
 
-    class Report
+    # body lines - fasta execution result
+    program, *hits = data.split(/\n>>/)
 
-      def initialize(data)
-        # header lines - brief list of the hits
-        if data.sub!(/.*\nThe best scores are/m, '')
-          data.sub!(/(.*)\n\n>>>/m, '')
-          @list = "The best scores are" + $1
-        else
-          data.sub!(/.*\n!!\s+/m, '')
-          data.sub!(/.*/) { |x| @list = x; '' }
-        end
+    # trailing lines - log messages of the execution
+    @log = hits.pop
+    @log.sub!(/.*<\n/m, '')
+    @log.strip!
 
-        # body lines - fasta execution result
-        program, *hits = data.split(/\n>>/)
+    # parse results
+    @program = Program.new(program)
+    @hits = []
 
-        # trailing lines - log messages of the execution
-        @log = hits.pop
-        @log.sub!(/.*<\n/m, '')
-        @log.strip!
+    hits.each do |x|
+      @hits.push(Hit.new(x))
+    end
+  end
+  
+  # Returns the 'The best scores are' lines as a String.
+  attr_reader :list
 
-        # parse results
-        @program = Program.new(program)
-        @hits = []
+  # Returns the trailing lines including library size, execution date,
+  # fasta function used, and fasta versions as a String.
+  attr_reader :log
 
-        hits.each do |x|
-          @hits.push(Hit.new(x))
-        end
-      end
-      attr_reader :list, :log, :program, :hits
+  # Returns a Bio::Fasta::Report::Program object.
+  attr_reader :program
 
-      def each
-        @hits.each do |x|
-          yield x
-        end
-      end
+  # Returns an Array of Bio::Fasta::Report::Hit objects.
+  attr_reader :hits
 
-      def threshold(evalue_max = 0.1)
-        list = []
-        @hits.each do |x|
-          list.push(x) if x.evalue < evalue_max
-        end
-        return list
-      end
+  # Iterates on each Bio::Fasta::Report::Hit object.
+  def each
+    @hits.each do |x|
+      yield x
+    end
+  end
 
-      def lap_over(length_min = 0)
-        list = []
-        @hits.each do |x|
-          list.push(x) if x.overlap > length_min
-        end
-        return list
-      end
+  # Returns an Array of Bio::Fasta::Report::Hit objects having
+  # better evalue than 'evalue_max'.
+  def threshold(evalue_max = 0.1)
+    list = []
+    @hits.each do |x|
+      list.push(x) if x.evalue < evalue_max
+    end
+    return list
+  end
 
+  # Returns an Array of Bio::Fasta::Report::Hit objects having
+  # longer overlap length than 'length_min'.
+  def lap_over(length_min = 0)
+    list = []
+    @hits.each do |x|
+      list.push(x) if x.overlap > length_min
+    end
+    return list
+  end
 
-      class Program
-        def initialize(data)
-          @definition, *program = data.split(/\n/)
-          @program = {}
+  # Log of the fasta execution environments.
+  class Program
+    def initialize(data)
+      @definition, *program = data.split(/\n/)
+      @program = {}
 
-          pat = /;\s+([^:]+):\s+(.*)/
+      pat = /;\s+([^:]+):\s+(.*)/
 
-          program.each do |x|
-            if pat.match(x)
-              @program[$1] = $2
-            end
-          end
+      program.each do |x|
+        if pat.match(x)
+          @program[$1] = $2
         end
-        attr_reader :definition, :program
       end
+    end
+    
+    # Returns a String containing query and library filenames.
+    attr_reader :definition
+
+    # Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv',
+    # 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup',
+    # 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values.
+    attr_reader :program
+  end
 
 
-      class Hit
-        def initialize(data)
-          score, query, target = data.split(/\n>/)
-
-          @definition, *score = score.split(/\n/)
-          @score = {}
+  class Hit
+    def initialize(data)
+      score, query, target = data.split(/\n>/)
 
-          pat = /;\s+([^:]+):\s+(.*)/
+      @definition, *score = score.split(/\n/)
+      @score = {}
 
-          score.each do |x|
-            if pat.match(x)
-              @score[$1] = $2
-            end
-          end
+      pat = /;\s+([^:]+):\s+(.*)/
 
-          @query = Query.new(query)
-          @target = Target.new(target)
-        end
-        attr_reader :definition, :score, :query, :target
-
-        def evalue
-          if @score['fa_expect']
-            @score['fa_expect'].to_f
-          elsif @score['sw_expect']
-            @score['sw_expect'].to_f
-          elsif @score['fx_expect']
-            @score['fx_expect'].to_f
-          elsif @score['tx_expect']
-            @score['tx_expect'].to_f
-          end
+      score.each do |x|
+        if pat.match(x)
+          @score[$1] = $2
         end
+      end
 
-        def bit_score
-          if @score['fa_bits']
-            @score['fa_bits'].to_f
-          elsif @score['sw_bits']
-            @score['sw_bits'].to_f
-          elsif @score['fx_bits']
-            @score['fx_bits'].to_f
-          elsif @score['tx_bits']
-            @score['tx_bits'].to_f
-          end
-        end
+      @query = Query.new(query)
+      @target = Target.new(target)
+    end
+    attr_reader :definition, :score, :query, :target
+
+    # E-value score
+    def evalue
+      if @score['fa_expect']
+        @score['fa_expect'].to_f
+      elsif @score['sw_expect']
+        @score['sw_expect'].to_f
+      elsif @score['fx_expect']
+        @score['fx_expect'].to_f
+      elsif @score['tx_expect']
+        @score['tx_expect'].to_f
+      end
+    end
 
-        def direction
-          @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
-        end
+    # Bit score
+    def bit_score
+      if @score['fa_bits']
+        @score['fa_bits'].to_f
+      elsif @score['sw_bits']
+        @score['sw_bits'].to_f
+      elsif @score['fx_bits']
+        @score['fx_bits'].to_f
+      elsif @score['tx_bits']
+        @score['tx_bits'].to_f
+      end
+    end
 
-        def sw
-          @score['sw_score'].to_i
-        end
+    def direction
+      @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
+    end
 
-        def identity
-          @score['sw_ident'].to_f
-        end
+    # Smith-Waterman score
+    def sw
+      @score['sw_score'].to_i
+    end
 
-        def overlap
-          @score['sw_overlap'].to_i
-        end
+    # percent identity
+    def identity
+      @score['sw_ident'].to_f
+    end
 
-        def query_id
-          @query.entry_id
-        end
+    # overlap length
+    def overlap
+      @score['sw_overlap'].to_i
+    end
 
-        def target_id
-          @target.entry_id
-        end
+    # Shortcuts for the methods of Bio::Fasta::Report::Hit::Query
 
-        def query_def
-          @query.definition
-        end
+    def query_id
+      @query.entry_id
+    end
 
-        def target_def
-          @target.definition
-        end
+    def target_id
+      @target.entry_id
+    end
 
-        def query_len
-          @query.length
-        end
+    def query_def
+      @query.definition
+    end
 
-        def target_len
-          @target.length
-        end
+    def target_def
+      @target.definition
+    end
 
-        def query_seq
-          @query.sequence
-        end
+    def query_len
+      @query.length
+    end
 
-        def target_seq
-          @target.sequence
-        end
+    # Shortcuts for the methods of Bio::Fasta::Report::Hit::Target
 
-        def query_type
-          @query.moltype
-        end
+    def target_len
+      @target.length
+    end
 
-        def target_type
-          @target.moltype
-        end
+    def query_seq
+      @query.sequence
+    end
 
-        def query_start
-          @query.start
-        end
+    def target_seq
+      @target.sequence
+    end
 
-        def query_end
-          @query.stop
-        end
+    def query_type
+      @query.moltype
+    end
 
-        def target_start
-          @target.start
-        end
+    def target_type
+      @target.moltype
+    end
 
-        def target_end
-          @target.stop
-        end
+    # Information on matching region
 
-        def lap_at
-          [ query_start, query_end, target_start, target_end ]
-        end
+    def query_start
+      @query.start
+    end
 
+    def query_end
+      @query.stop
+    end
 
-        class Query
-          def initialize(data)
-            @definition, *data = data.split(/\n/)
-            @data = {}
-            @sequence = ''
+    def target_start
+      @target.start
+    end
 
-            pat = /;\s+([^:]+):\s+(.*)/
+    def target_end
+      @target.stop
+    end
 
-            data.each do |x|
-              if pat.match(x)
-                @data[$1] = $2
-              else
-                @sequence += x
-              end
-            end
-          end
-          attr_reader :definition, :data, :sequence
+    def lap_at
+      [ query_start, query_end, target_start, target_end ]
+    end
 
-          def entry_id
-            @definition[/\S+/]
-          end
 
-          def length
-            @data['sq_len'].to_i
-          end
+    class Query
+      def initialize(data)
+        @definition, *data = data.split(/\n/)
+        @data = {}
+        @sequence = ''
 
-          def moltype
-            @data['sq_type']
-          end
+        pat = /;\s+([^:]+):\s+(.*)/
 
-          def start
-            @data['al_start'].to_i
+        data.each do |x|
+          if pat.match(x)
+            @data[$1] = $2
+          else
+            @sequence += x
           end
+        end
+      end
 
-          def stop
-            @data['al_stop'].to_i
-          end
+      # Returns the definition of the entry as a String.
+      # You can access this value by Report::Hit#query_def method.
+      attr_reader :definition
 
-        end
+      # Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type',
+      # 'al_start', 'al_stop', and 'al_display_start' values.
+      # You can access most of these values by Report::Hit#query_* methods.
+      attr_reader :data
+
+      # Returns the sequence (with gaps) as a String.
+      # You can access this value by the Report::Hit#query_seq method.
+      attr_reader :sequence
 
-        class Target < Query; end
+      # Returns the first word in the definition as a String.
+      # You can get this value by Report::Hit#query_id method.
+      def entry_id
+        @definition[/\S+/]
+      end
+
+      # Returns the sequence length.
+      # You can access this value by the Report::Hit#query_len method.
+      def length
+        @data['sq_len'].to_i
+      end
+
+      # Returns 'p' for protein sequence, 'D' for nucleotide sequence.
+      def moltype
+        @data['sq_type']
+      end
+
+      # Returns alignment start position. You can also access this value
+      # by Report::Hit#query_start method for shortcut.
+      def start
+        @data['al_start'].to_i
+      end
+
+      # Returns alignment end position. You can access this value
+      # by Report::Hit#query_end method for shortcut.
+      def stop
+        @data['al_stop'].to_i
       end
 
     end
 
+    # Same as Bio::Fasta::Report::Hit::Query but for Target.
+    class Target < Query; end
   end
-end
+
+end # Report
+
+end # Fasta
+end # Bio
 
 
 if __FILE__ == $0
@@ -278,151 +323,3 @@ if __FILE__ == $0
 end
 
 
-=begin
-
-= Bio::Fasta::Report
-
-Summarized results of the fasta execution hits.
-
---- Bio::Fasta::Report.new(data)
---- Bio::Fasta::Report#each
-
-      Iterates on each Bio::Fasta::Report::Hit object.
-
---- Bio::Fasta::Report#hits
-
-      Returns an Array of Bio::Fasta::Report::Hit objects.
-
---- Bio::Fasta::Report#threshold(evalue_max = 0.1)
-
-      Returns an Array of Bio::Fasta::Report::Hit objects having
-      better evalue than 'evalue_max'.
-
---- Bio::Fasta::Report#lap_over(length_min = 0)
-
-      Returns an Array of Bio::Fasta::Report::Hit objects having
-      longer overlap length than 'length_min'.
-
---- Bio::Fasta::Report#program
-
-      Returns a Bio::Fasta::Report::Program object.
-
---- Bio::Fasta::Report#list
-
-      Returns the 'The best scores are' lines as a String.
-
---- Bio::Fasta::Report#log
-
-      Returns the trailing lines including library size, execution date,
-      fasta function used, and fasta versions as a String.
-
-
-== Bio::Fasta::Report::Program
-
-Log of the fasta execution environments.
-
---- Bio::Fasta::Report::Program#definition
-
-      Returns a String containing query and library filenames.
-
---- Bio::Fasta::Report::Program#program
-
-      Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv',
-      'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup',
-      'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values.
-
-
-== Bio::Fasta::Report::Hit
-
---- Bio::Fasta::Report::Hit#definition
---- Bio::Fasta::Report::Hit#score
---- Bio::Fasta::Report::Hit#query
---- Bio::Fasta::Report::Hit#target
-
-      Accessors for the internal structures.
-
---- Bio::Fasta::Report::Hit#evalue
---- Bio::Fasta::Report::Hit#bit_score
---- Bio::Fasta::Report::Hit#sw
---- Bio::Fasta::Report::Hit#identity
-
-      Matching scores.
-
---- Bio::Fasta::Report::Hit#query_id
---- Bio::Fasta::Report::Hit#query_def
---- Bio::Fasta::Report::Hit#query_len
---- Bio::Fasta::Report::Hit#query_seq
---- Bio::Fasta::Report::Hit#query_type
---- Bio::Fasta::Report::Hit#target_id
---- Bio::Fasta::Report::Hit#target_def
---- Bio::Fasta::Report::Hit#target_len
---- Bio::Fasta::Report::Hit#target_seq
---- Bio::Fasta::Report::Hit#target_type
-
-      Matching subjects.
-      Shortcuts for the methods of Hit::Query and the Hit::Target.
-
---- Bio::Fasta::Report::Hit#query_start
---- Bio::Fasta::Report::Hit#query_end
---- Bio::Fasta::Report::Hit#target_start
---- Bio::Fasta::Report::Hit#target_end
---- Bio::Fasta::Report::Hit#overlap
---- Bio::Fasta::Report::Hit#lap_at
---- Bio::Fasta::Report::Hit#direction
-
-      Matching regions.
-
-
-== Bio::Fasta::Report::Hit::Query
-
---- Bio::Fasta::Report::Hit::Query#entry_id
-
-      Returns the first word in the definition as a String.
-      You can get this value by Report::Hit#query_id method.
-
---- Bio::Fasta::Report::Hit::Query#definition
-
-      Returns the definition of the entry as a String.
-      You can access this value by Report::Hit#query_def method.
-
---- Bio::Fasta::Report::Hit::Query#sequence
-
-      Returns the sequence (with gaps) as a String.
-      You can access this value by the Report::Hit#query_seq method.
-
---- Bio::Fasta::Report::Hit::Query#length
-
-      Returns the sequence length.
-      You can access this value by the Report::Hit#query_len method.
-
---- Bio::Fasta::Report::Hit::Query#moltype
-
-      Returns 'p' for protein sequence, 'D' for nucleotide sequence.
-
---- Bio::Fasta::Report::Hit::Query#start
---- Bio::Fasta::Report::Hit::Query#stop
-
-      Returns alignment start and stop position.
-      You can access these values by Report::Hit#query_start and
-      Report::Hit#query_end methods.
-
---- Bio::Fasta::Report::Hit::Query#data
-
-      Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type',
-      'al_start', 'al_stop', and 'al_display_start' values.
-      You can access most of these values by Report::Hit#query_* methods.
-
-
-== Bio::Fasta::Report::Hit::Target
-
---- Bio::Fasta::Report::Hit::Target#entry_id
---- Bio::Fasta::Report::Hit::Target#definition
---- Bio::Fasta::Report::Hit::Target#data
---- Bio::Fasta::Report::Hit::Target#sequence
---- Bio::Fasta::Report::Hit::Target#length
---- Bio::Fasta::Report::Hit::Target#start
---- Bio::Fasta::Report::Hit::Target#stop
-
-      Same as Bio::Fasta::Report::Hit::Query but for Target.
-
-=end