bio 0.7.0

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

@@ -0,0 +1,428 @@
+#
+# bio/appl/fasta/format10.rb - FASTA output (-m 10) parser
+# 
+#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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 $
+#
+
+require 'bio/appl/fasta'
+
+module Bio
+  class Fasta
+
+    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
+
+        # body lines - fasta execution result
+        program, *hits = data.split(/\n>>/)
+
+        # trailing lines - log messages of the execution
+        @log = hits.pop
+        @log.sub!(/.*<\n/m, '')
+        @log.strip!
+
+        # parse results
+        @program = Program.new(program)
+        @hits = []
+
+        hits.each do |x|
+          @hits.push(Hit.new(x))
+        end
+      end
+      attr_reader :list, :log, :program, :hits
+
+      def each
+        @hits.each do |x|
+          yield x
+        end
+      end
+
+      def threshold(evalue_max = 0.1)
+        list = []
+        @hits.each do |x|
+          list.push(x) if x.evalue < evalue_max
+        end
+        return list
+      end
+
+      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 = {}
+
+          pat = /;\s+([^:]+):\s+(.*)/
+
+          program.each do |x|
+            if pat.match(x)
+              @program[$1] = $2
+            end
+          end
+        end
+        attr_reader :definition, :program
+      end
+
+
+      class Hit
+        def initialize(data)
+          score, query, target = data.split(/\n>/)
+
+          @definition, *score = score.split(/\n/)
+          @score = {}
+
+          pat = /;\s+([^:]+):\s+(.*)/
+
+          score.each do |x|
+            if pat.match(x)
+              @score[$1] = $2
+            end
+          end
+
+          @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
+        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
+
+        def direction
+          @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
+        end
+
+        def sw
+          @score['sw_score'].to_i
+        end
+
+        def identity
+          @score['sw_ident'].to_f
+        end
+
+        def overlap
+          @score['sw_overlap'].to_i
+        end
+
+        def query_id
+          @query.entry_id
+        end
+
+        def target_id
+          @target.entry_id
+        end
+
+        def query_def
+          @query.definition
+        end
+
+        def target_def
+          @target.definition
+        end
+
+        def query_len
+          @query.length
+        end
+
+        def target_len
+          @target.length
+        end
+
+        def query_seq
+          @query.sequence
+        end
+
+        def target_seq
+          @target.sequence
+        end
+
+        def query_type
+          @query.moltype
+        end
+
+        def target_type
+          @target.moltype
+        end
+
+        def query_start
+          @query.start
+        end
+
+        def query_end
+          @query.stop
+        end
+
+        def target_start
+          @target.start
+        end
+
+        def target_end
+          @target.stop
+        end
+
+        def lap_at
+          [ query_start, query_end, target_start, target_end ]
+        end
+
+
+        class Query
+          def initialize(data)
+            @definition, *data = data.split(/\n/)
+            @data = {}
+            @sequence = ''
+
+            pat = /;\s+([^:]+):\s+(.*)/
+
+            data.each do |x|
+              if pat.match(x)
+                @data[$1] = $2
+              else
+                @sequence += x
+              end
+            end
+          end
+          attr_reader :definition, :data, :sequence
+
+          def entry_id
+            @definition[/\S+/]
+          end
+
+          def length
+            @data['sq_len'].to_i
+          end
+
+          def moltype
+            @data['sq_type']
+          end
+
+          def start
+            @data['al_start'].to_i
+          end
+
+          def stop
+            @data['al_stop'].to_i
+          end
+
+        end
+
+        class Target < Query; end
+      end
+
+    end
+
+  end
+end
+
+
+if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue
+  end
+
+  rep = Bio::Fasta::Report.new(ARGF.read)
+  p rep
+
+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

data/lib/bio/appl/fasta/format6.rb

@@ -0,0 +1,37 @@
+#
+# bio/appl/fasta/format6.rb - FASTA output (-m 6) parser
+# 
+#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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: format6.rb,v 1.2 2005/09/08 01:22:09 k Exp $
+#
+
+module Bio
+  class Fasta
+
+    class Report
+
+      # will be ported from sample/{fasta2tab,ssearch2tab,tfastx2tab}.rb
+
+      def initialize
+        raise NotImplementedError
+      end
+    end
+
+  end
+end
+