pepxml.rb in ms-ident-0.0.21

- old
+ new

@@ -20,10 +20,39 @@
   DEFAULT_PEPXML_VERSION = MsmsPipelineAnalysis::PEPXML_VERSION
   XML_ENCODING = 'UTF-8'
 
   attr_accessor :msms_pipeline_analysis
 
+  def self.search_hits(file)
+    fields = [:aaseq, :charge]
+    ss_names = []
+    have_ss_names = false
+    # begin with aaseq, charge
+    hit_values = File.open(file) do |io|
+      doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS)
+      # we can work with namespaces, or just remove them ...
+      doc.remove_namespaces!
+      root = doc.root
+      search_hits = root.xpath('//search_hit')
+      search_hits.map do |search_hit| 
+        aaseq = search_hit['peptide']
+        charge = search_hit.parent.parent['assumed_charge'].to_i
+        search_score_nodes = search_hit.children.select {|node| node.name == 'search_score' }
+        ss_values = []
+        search_score_nodes.each do |node|
+          ss_names << node['name'].to_sym unless have_ss_names
+          ss_values << node['value'].to_f
+        end
+        have_ss_names = true
+        [aaseq, charge, *ss_values]
+      end
+    end
+    fields.push(*ss_names)
+    peptide_hit_class = Struct.new(*fields)
+    hit_values.map {|ar| peptide_hit_class.new(*ar) }
+  end
+
   def pepxml_version
     msms_pipeline_analysis.pepxml_version
   end
 
   # returns an array of spectrum queries
@@ -40,10 +69,10 @@
   def add_stylesheet(doc, location)
     xml_stylesheet = Nokogiri::XML::ProcessingInstruction.new(doc, "xml-stylesheet", %Q{type="text/xsl" href="#{location}"})
     doc.root.add_previous_sibling  xml_stylesheet
     doc
   end
-  
+
   # if no options are given, an xml string is returned.  If either :outdir or
   # :outfile is given, the xml is written to file and the output filename is returned.
   # A single string argument will be interpreted as :outfile if it ends in
   # '.xml' and the :outdir otherwise.  In this case, update_summary_xml is still true
   #