bio 1.0.0 → 1.1.0

data/lib/bio/appl/blast/rexml.rb

@@ -1,24 +1,15 @@
 #
-# bio/appl/blast/rexml.rb - BLAST XML output (-m 7) parser by REXML
+# = bio/appl/blast/rexml.rb - BLAST XML output (-m 7) parser by REXML
 # 
-#   Copyright (C) 2002,2003 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2002, 2003 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: rexml.rb,v 1.10 2005/09/08 01:22:08 k Exp $
+# $Id: rexml.rb,v 1.12 2007/04/05 23:35:39 trevor Exp $
 #
+# == Note
+# 
+# This file is automatically loaded by bio/appl/blast/report.rb
+# 
 
 begin
   require 'rexml/document'
@@ -144,8 +135,3 @@ module Bio
 end
 
 
-=begin
-
-This file is automatically loaded by bio/appl/blast/report.rb
-
-=end

data/lib/bio/appl/blast/wublast.rb

@@ -1,19 +1,22 @@
 #
 # = bio/appl/blast/wublast.rb - WU-BLAST default output parser
 # 
-# Copyright:: Copyright (C) 2003 GOTO Naohisa <ng@bioruby.org>
-# License:: Ruby's
+# Copyright::  Copyright (C) 2003 GOTO Naohisa <ng@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: wublast.rb,v 1.6 2006/02/22 08:46:15 ngoto Exp $
+# $Id: wublast.rb,v 1.11 2007/04/21 08:58:17 ngoto Exp $
 #
-#  WU-BLAST default output parser.
+# == Description
 #
-#  The parser is still incomplete and may contain many bugs,
-#  because I didn't have WU-BLAST license.
-#  It was tested under web-based WU-BLAST results and
-#  obsolete version downloaded from http://blast.wustl.edu/ .
+# WU-BLAST default output parser.
+#
+# The parser is still incomplete and may contain many bugs,
+# because I didn't have WU-BLAST license.
+# It was tested under web-based WU-BLAST results and
+# obsolete version downloaded from http://blast.wustl.edu/ .
+#
+# == References
 #
-# = References
 # * http://blast.wustl.edu/
 # * http://www.ebi.ac.uk/blast2/
 #
@@ -134,6 +137,10 @@ module Bio
                 end
               end
             end
+            if ev = @parameters['E'] then
+              ev = '1' + ev if ev[0] == ?e
+              @parameters['E'] = ev.to_f
+            end
             @parse_parameters = true
           end
         end
@@ -245,10 +252,12 @@ module Bio
                     @hits[i] = h
                   end
                   z.pop if flag_tblast #ignore Reading Frame
-                  scr = z.pop.to_s
+                  scr = z.pop
+                  scr = (scr ? scr.to_i : nil)
                   pval = z.pop.to_s
+                  pval = '1' + pval if pval[0] == ?e
+                  pval = (pval.empty? ? (1.0/0.0) : pval.to_f)
                   nnum = z.pop.to_i
-                  #ev = '1' + ev if ev[0] == ?e
                   h.instance_eval {
                     @score = scr
                     @pvalue = pval
@@ -280,7 +289,7 @@ module Bio
                 data.shift
                 r = data.first
               end
-              if /^\s+Score/ =~ r then
+              if /\A\s+Score/ =~ r then
                 @hsps << HSP.new(data)
               else
                 break

data/lib/bio/appl/blast/xmlparser.rb

@@ -1,24 +1,22 @@
 #
-# bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
+# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
 # 
-#   Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org>
-#   Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2001 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2003 
+#              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.
+# $Id: xmlparser.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
 #
-#  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
+# == Description
+# 
+# A parser for blast XML report (format 7) based on the XMLParser.
+# This file is automatically loaded by bio/appl/blast/report.rb if
+# the XMLParser installed.
 #
-#  $Id: xmlparser.rb,v 1.13 2005/09/08 01:22:08 k Exp $
+# BioRuby provides two implements of the paser for the blast XML format report
+# (format 7) based on the XMLParser and the REXML.
 #
 
 begin
@@ -27,192 +25,191 @@ rescue LoadError
 end
 
 module Bio
-  class Blast
-    class Report
-
-      private
-
-      def xmlparser_parse(xml)
-        parser = XMLParser.new
-        def parser.default; end
-        
-        begin
-          tag_stack = Array.new
-          hash = Hash.new
-
-          parser.parse(xml) do |type, name, data|
-            #print "type=#{type.inspect} name=#{name.inspect} data=#{data.inspect}\n" # for DEBUG
-            case type
-            when XMLParser::START_ELEM
-              tag_stack.push(name)
-              hash.update(data)
-              case name
-              when 'Iteration'
-                iteration = Iteration.new
-                @iterations.push(iteration)
-              when 'Hit'
-                hit = Hit.new
-                hit.query_id = @query_id
-                hit.query_def = @query_def
-                hit.query_len = @query_len
-                @iterations.last.hits.push(hit)
-              when 'Hsp'
-                hsp = Hsp.new
-                @iterations.last.hits.last.hsps.push(hsp)
-              end
-            when XMLParser::END_ELEM
-              case name
-              when /^BlastOutput/
-                xmlparser_parse_program(name,hash)
-                hash = Hash.new
-              when /^Parameters$/
-                xmlparser_parse_parameters(hash)
-                hash = Hash.new
-              when /^Iteration/
-                xmlparser_parse_iteration(name, hash)
-                hash = Hash.new
-              when /^Hit/
-                xmlparser_parse_hit(name, hash)
-                hash = Hash.new
-              when /^Hsp$/
-                xmlparser_parse_hsp(hash)
-                hash = Hash.new
-              when /^Statistics$/
-                xmlparser_parse_statistics(hash)
-                hash = Hash.new
-              end
-              tag_stack.pop
-            when XMLParser::CDATA
-              if hash[tag_stack.last].nil?
-                hash[tag_stack.last] = data unless data.strip.empty?
-              else
-                hash[tag_stack.last].concat(data) if data
-              end
-            when XMLParser::PI
+class Blast
+  class Report
+
+    private
+
+    def xmlparser_parse(xml)
+      parser = XMLParser.new
+      def parser.default; end
+       
+      begin
+        tag_stack = Array.new
+        hash = Hash.new
+
+        parser.parse(xml) do |type, name, data|
+          case type
+          when XMLParser::START_ELEM
+            tag_stack.push(name)
+            hash.update(data)
+            case name
+            when 'Iteration'
+              iteration = Iteration.new
+              @iterations.push(iteration)
+            when 'Hit'
+              hit = Hit.new
+              hit.query_id = @query_id
+              hit.query_def = @query_def
+              hit.query_len = @query_len
+              @iterations.last.hits.push(hit)
+            when 'Hsp'
+              hsp = Hsp.new
+              @iterations.last.hits.last.hsps.push(hsp)
+            end
+          when XMLParser::END_ELEM
+            case name
+            when /^BlastOutput/
+              xmlparser_parse_program(name,hash)
+              hash = Hash.new
+            when /^Parameters$/
+              xmlparser_parse_parameters(hash)
+              hash = Hash.new
+            when /^Iteration/
+              xmlparser_parse_iteration(name, hash)
+              hash = Hash.new
+            when /^Hit/
+              xmlparser_parse_hit(name, hash)
+              hash = Hash.new
+            when /^Hsp$/
+              xmlparser_parse_hsp(hash)
+              hash = Hash.new
+            when /^Statistics$/
+              xmlparser_parse_statistics(hash)
+              hash = Hash.new
             end
+            tag_stack.pop
+          when XMLParser::CDATA
+            if hash[tag_stack.last].nil?
+              hash[tag_stack.last] = data unless data.strip.empty?
+            else
+              hash[tag_stack.last].concat(data) if data
+            end
+          when XMLParser::PI
           end
-        rescue XMLParserError
-          line = parser.line
-          column = parser.column
-          print "Parse error at #{line}(#{column}) : #{$!}\n"
         end
+      rescue XMLParserError
+        line = parser.line
+        column = parser.column
+        print "Parse error at #{line}(#{column}) : #{$!}\n"
       end
+    end
 
 
-      def xmlparser_parse_program(tag, hash)
-        case tag
-        when 'BlastOutput_program'
-          @program = hash[tag]
-        when 'BlastOutput_version'
-          @version = hash[tag]
-        when 'BlastOutput_reference'
-          @reference = hash[tag]
-        when 'BlastOutput_db'
-          @db = hash[tag].strip
-        when 'BlastOutput_query-ID'
-          @query_id = hash[tag]
-        when 'BlastOutput_query-def'
-          @query_def = hash[tag]
-        when 'BlastOutput_query-len'
-          @query_len = hash[tag].to_i
-        end
+    def xmlparser_parse_program(tag, hash)
+      case tag
+      when 'BlastOutput_program'
+        @program = hash[tag]
+      when 'BlastOutput_version'
+        @version = hash[tag]
+      when 'BlastOutput_reference'
+        @reference = hash[tag]
+      when 'BlastOutput_db'
+        @db = hash[tag].strip
+      when 'BlastOutput_query-ID'
+        @query_id = hash[tag]
+      when 'BlastOutput_query-def'
+        @query_def = hash[tag]
+      when 'BlastOutput_query-len'
+        @query_len = hash[tag].to_i
       end
+    end
 
-      def xmlparser_parse_parameters(hash)
-        labels = { 
-          'matrix'	=> 'Parameters_matrix',
-          'expect'	=> 'Parameters_expect',
-          'include'	=> 'Parameters_include',
-          'sc-match'	=> 'Parameters_sc-match',
-          'sc-mismatch'	=> 'Parameters_sc-mismatch',
-          'gap-open'	=> 'Parameters_gap-open',
-          'gap-extend'	=> 'Parameters_gap-extend',
-          'filter'	=> 'Parameters_filter',
-          'pattern'	=> 'Parameters_pattern',
-          'entrez-query'=> 'Parameters_entrez-query',
-        }
-        labels.each do |k,v|
-          case k
-          when 'filter', 'matrix'
-            @parameters[k] = hash[v].to_s
-          else
-            @parameters[k] = hash[v].to_i
-          end
+    def xmlparser_parse_parameters(hash)
+      labels = { 
+        'matrix'       => 'Parameters_matrix',
+        'expect'       => 'Parameters_expect',
+        'include'      => 'Parameters_include',
+        'sc-match'     => 'Parameters_sc-match',
+        'sc-mismatch'  => 'Parameters_sc-mismatch',
+        'gap-open'     => 'Parameters_gap-open',
+        'gap-extend'   => 'Parameters_gap-extend',
+        'filter'       => 'Parameters_filter',
+        'pattern'      => 'Parameters_pattern',
+        'entrez-query' => 'Parameters_entrez-query',
+      }
+      labels.each do |k,v|
+        case k
+        when 'filter', 'matrix'
+          @parameters[k] = hash[v].to_s
+        else
+          @parameters[k] = hash[v].to_i
         end
       end
+    end
 
-      def xmlparser_parse_iteration(tag, hash)
-        case tag
-        when 'Iteration_iter-num'
-          @iterations.last.num = hash[tag].to_i
-        when 'Iteration_message'
-          @iterations.last.message = hash[tag].to_s
-        end
+    def xmlparser_parse_iteration(tag, hash)
+      case tag
+      when 'Iteration_iter-num'
+        @iterations.last.num = hash[tag].to_i
+      when 'Iteration_message'
+        @iterations.last.message = hash[tag].to_s
       end
+    end
 
-      def xmlparser_parse_hit(tag, hash)
-        hit = @iterations.last.hits.last
-        case tag
-        when 'Hit_num'
-          hit.num = hash[tag].to_i
-        when 'Hit_id'
-          hit.hit_id = hash[tag].clone
-        when 'Hit_def'
-          hit.definition = hash[tag].clone
-        when 'Hit_accession'
-          hit.accession = hash[tag].clone
-        when 'Hit_len'
-          hit.len = hash[tag].clone.to_i
-        end
+    def xmlparser_parse_hit(tag, hash)
+      hit = @iterations.last.hits.last
+      case tag
+      when 'Hit_num'
+        hit.num = hash[tag].to_i
+      when 'Hit_id'
+        hit.hit_id = hash[tag].clone
+      when 'Hit_def'
+        hit.definition = hash[tag].clone
+      when 'Hit_accession'
+        hit.accession = hash[tag].clone
+      when 'Hit_len'
+        hit.len = hash[tag].clone.to_i
       end
+    end
 
-      def xmlparser_parse_hsp(hash)
-        hsp = @iterations.last.hits.last.hsps.last
-        hsp.num			= hash['Hsp_num'].to_i
-        hsp.bit_score		= hash['Hsp_bit-score'].to_f
-        hsp.score		= hash['Hsp_score'].to_i
-        hsp.evalue		= hash['Hsp_evalue'].to_f
-        hsp.query_from		= hash['Hsp_query-from'].to_i
-        hsp.query_to		= hash['Hsp_query-to'].to_i
-        hsp.hit_from		= hash['Hsp_hit-from'].to_i
-        hsp.hit_to		= hash['Hsp_hit-to'].to_i
-        hsp.pattern_from	= hash['Hsp_pattern-from'].to_i
-        hsp.pattern_to		= hash['Hsp_pattern-to'].to_i
-   	hsp.query_frame		= hash['Hsp_query-frame'].to_i
-        hsp.hit_frame		= hash['Hsp_hit-frame'].to_i
-        hsp.identity		= hash['Hsp_identity'].to_i
-        hsp.positive		= hash['Hsp_positive'].to_i
-        hsp.gaps		= hash['Hsp_gaps'].to_i
-        hsp.align_len		= hash['Hsp_align-len'].to_i
-        hsp.density		= hash['Hsp_density'].to_i
-        hsp.qseq		= hash['Hsp_qseq']
-        hsp.hseq		= hash['Hsp_hseq']
-        hsp.midline		= hash['Hsp_midline']
-      end
+    def xmlparser_parse_hsp(hash)
+      hsp = @iterations.last.hits.last.hsps.last
+      hsp.num          = hash['Hsp_num'].to_i
+      hsp.bit_score    = hash['Hsp_bit-score'].to_f
+      hsp.score        = hash['Hsp_score'].to_i
+      hsp.evalue       = hash['Hsp_evalue'].to_f
+      hsp.query_from   = hash['Hsp_query-from'].to_i
+      hsp.query_to     = hash['Hsp_query-to'].to_i
+      hsp.hit_from     = hash['Hsp_hit-from'].to_i
+      hsp.hit_to       = hash['Hsp_hit-to'].to_i
+      hsp.pattern_from = hash['Hsp_pattern-from'].to_i
+      hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
+      hsp.query_frame  = hash['Hsp_query-frame'].to_i
+      hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
+      hsp.identity     = hash['Hsp_identity'].to_i
+      hsp.positive     = hash['Hsp_positive'].to_i
+      hsp.gaps         = hash['Hsp_gaps'].to_i
+      hsp.align_len    = hash['Hsp_align-len'].to_i
+      hsp.density      = hash['Hsp_density'].to_i
+      hsp.qseq         = hash['Hsp_qseq']
+      hsp.hseq         = hash['Hsp_hseq']
+      hsp.midline      = hash['Hsp_midline']
+    end
 
-      def xmlparser_parse_statistics(hash)
-        labels = {
-          'db-num'	=> 'Statistics_db-num',
-          'db-len'	=> 'Statistics_db-len',
-          'hsp-len'	=> 'Statistics_hsp-len',
-          'eff-space'	=> 'Statistics_eff-space',
-          'kappa'	=> 'Statistics_kappa',
-          'lambda'	=> 'Statistics_lambda',
-          'entropy'	=> 'Statistics_entropy'
-        }
-        labels.each do |k,v|
-          case k
-          when 'db-num', 'db-len', 'hsp-len'
-            @iterations.last.statistics[k] = hash[v].to_i
-          else
-            @iterations.last.statistics[k] = hash[v].to_f
-          end
+    def xmlparser_parse_statistics(hash)
+      labels = {
+        'db-num'	=> 'Statistics_db-num',
+        'db-len'	=> 'Statistics_db-len',
+        'hsp-len'	=> 'Statistics_hsp-len',
+        'eff-space'	=> 'Statistics_eff-space',
+        'kappa'	=> 'Statistics_kappa',
+        'lambda'	=> 'Statistics_lambda',
+        'entropy'	=> 'Statistics_entropy'
+      }
+      labels.each do |k,v|
+        case k
+        when 'db-num', 'db-len', 'hsp-len'
+          @iterations.last.statistics[k] = hash[v].to_i
+        else
+          @iterations.last.statistics[k] = hash[v].to_f
         end
       end
-        
     end
-  end
-end
+        
+  end # class Report
+end # class Blast
+end # module Bio
 
 
 =begin