ngoto-bio 1.2.9.9001

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

@@ -0,0 +1,236 @@
+#
+# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
+# 
+# Copyright::  Copyright (C) 2001 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2003 
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+# == 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.
+#
+# BioRuby provides two implements of the paser for the blast XML format report
+# (format 7) based on the XMLParser and the REXML.
+#
+
+begin
+  require 'xmlparser'
+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|
+          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$/
+              xmlparser_parse_statistics(hash)
+              hash = Hash.new
+            end
+            tag_stack.pop
+          when XMLParser::CDATA
+            if hash[tag_stack.last].nil?
+              hash[tag_stack.last] = data unless data.strip.empty?
+            else
+              hash[tag_stack.last].concat(data) if data
+            end
+          when XMLParser::PI
+          end
+        end
+      rescue XMLParserError
+        line = parser.line
+        column = parser.column
+        print "Parse error at #{line}(#{column}) : #{$!}\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
+    end
+
+    # set parameter of the key as val
+    def xml_set_parameter(key, val)
+      #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',
+      #}
+      k = key.sub(/\AParameters\_/, '')
+      @parameters[k] =
+        case k
+        when 'expect', 'include'
+          val.to_f
+        when /\Agap\-/, /\Asc\-/
+          val.to_i
+        else
+          val
+        end
+    end
+
+    def xmlparser_parse_parameters(hash)
+      hash.each do |k, v|
+        xml_set_parameter(k, v)
+      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
+
+        # for new BLAST XML format
+      when 'Iteration_query-ID'
+        @iterations.last.query_id = hash[tag].to_s
+      when 'Iteration_query-def'
+        @iterations.last.query_def = hash[tag].to_s
+      when 'Iteration_query-len'
+        @iterations.last.query_len = hash[tag].to_i
+      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
+    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
+      end
+    end
+        
+  end # class Report
+end # class Blast
+end # module Bio
+
+
+=begin
+
+This file is automatically loaded by bio/appl/blast/report.rb
+
+=end