Class: Mspire::Ident::Pepxml

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/ident/pepxml.rb,
lib/mspire/ident/pepxml/parameters.rb,
lib/mspire/ident/pepxml/search_hit.rb,
lib/mspire/ident/pepxml/modifications.rb,
lib/mspire/ident/pepxml/sample_enzyme.rb,
lib/mspire/ident/pepxml/search_result.rb,
lib/mspire/ident/pepxml/search_summary.rb,
lib/mspire/ident/pepxml/spectrum_query.rb,
lib/mspire/ident/pepxml/search_database.rb,
lib/mspire/ident/pepxml/msms_run_summary.rb,
lib/mspire/ident/pepxml/msms_pipeline_analysis.rb,
lib/mspire/ident/pepxml/search_hit/modification_info.rb

Defined Under Namespace

Classes: AminoacidModification, EnzymaticSearchConstraint, MsmsPipelineAnalysis, MsmsRunSummary, Parameters, SampleEnzyme, SearchDatabase, SearchHit, SearchResult, SearchSummary, SpectrumQuery, TerminalModification

Constant Summary collapse

XML_STYLESHEET_LOCATION = 
'/tools/bin/TPP/tpp/schema/pepXML_std.xsl'
DEFAULT_PEPXML_VERSION = 
MsmsPipelineAnalysis::PEPXML_VERSION
XML_ENCODING = 
'UTF-8'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(&block) ⇒ Pepxml

yields a new Msms_Pipeline_Analysis object if given a block



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# File 'lib/mspire/ident/pepxml.rb', line 73

def initialize(&block)
  block.call(@msms_pipeline_analysis=MsmsPipelineAnalysis.new) if block
end

Instance Attribute Details

#msms_pipeline_analysis ⇒ Object

Returns the value of attribute msms_pipeline_analysis.



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# File 'lib/mspire/ident/pepxml.rb', line 25

def msms_pipeline_analysis
  @msms_pipeline_analysis
end

Class Method Details

.simple_search_hits(file, &block) ⇒ Object

returns an array of Mspire::Ident::Pepxml::SearchHit::Simple structs will only process last result if duplicate search scores are included. Score keys returned as symbols and values cast as Floats while analysis results are all returned as strings.



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# File 'lib/mspire/ident/pepxml.rb', line 31

def self.simple_search_hits(file, &block)
  hit_values = File.open(file) do |io|
    doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS | Nokogiri::XML::ParseOptions::STRICT)
    # we can work with namespaces, or just remove them ...
    doc.remove_namespaces!
    root = doc.root
    search_hits = root.xpath('//search_hit')
    search_hits.each_with_index.map do |search_hit,i| 
      aaseq = search_hit['peptide']
      charge = search_hit.parent.parent['assumed_charge'].to_i
      nodes_by_name = search_hit.children.group_by(&:name)
      search_scores = {}
      nodes_by_name['search_score'].each do |node|
        search_scores[node['name'].to_sym] = node['value'].to_f
      end
      analysis_results = {}
      nodes_by_name['analysis_result'].each do |node|
        analysis_results[node['analysis']] = node.children.map do |atnode| 
          atnode.attribute_nodes.each_with_object({}) do |attribute, hash|
            hash[attribute.name] = attribute.value
          end
        end
      end
      hit = Mspire::Ident::Pepxml::SearchHit::Simple.new("hit_#{i}", Mspire::Ident::Search.new(file.chomp(File.extname(file))), aaseq, charge, search_scores, analysis_results)
      if block
        block.call(search_hit_n.parent.parent)
      end
      hit
    end
  end
end

Instance Method Details

#add_stylesheet(doc, location) ⇒ Object

takes an xml document object and sets it with the xml stylesheet



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# File 'lib/mspire/ident/pepxml.rb', line 78

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

#pepxml_version ⇒ Object 



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# File 'lib/mspire/ident/pepxml.rb', line 63

def pepxml_version
  msms_pipeline_analysis.pepxml_version
end

#spectrum_queries ⇒ Object

returns an array of spectrum queries



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# File 'lib/mspire/ident/pepxml.rb', line 68

def spectrum_queries
  msms_pipeline_analysis.msms_run_summary.spectrum_queries
end

#to_xml(opts = {}) ⇒ Object

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

options:

arg                    default
:outdir             => nil   write to disk using this outdir with summary_xml basename
:outfile            => nil   write to this filename (overrides outdir)
:update_summary_xml => true  update summary_xml attribute to point to the output file true/false

set outdir to File.dirname(pepxml_obj.msms_pipeline_analysis.msms_run_summary.base_name) to write to the same directory as the input search file.



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# File 'lib/mspire/ident/pepxml.rb', line 99

def to_xml(opts={})
  opts ||= {}
  if opts.is_a?(String) 
    opts = ( opts.match(/\.xml$/) ?  {:outfile => opts} : {:outdir => opts } )
  end
  opt = {:update_summary_xml => true, :outdir => nil, :outfile => nil}.merge(opts)

  if opt[:outfile]
    outfile = opt[:outfile]
  elsif opt[:outdir]
    outfile = File.join(opt[:outdir], msms_pipeline_analysis.summary_xml.split(/[\/\\]/).last)
  end
  self.msms_pipeline_analysis.summary_xml = File.expand_path(outfile) if (opt[:update_summary_xml] && outfile)

  builder = Nokogiri::XML::Builder.new(:encoding => XML_ENCODING)
  msms_pipeline_analysis.to_xml(builder)
  add_stylesheet(builder.doc, Mspire::Ident::Pepxml::XML_STYLESHEET_LOCATION)
  string = builder.doc.to_xml

  if outfile 
    File.open(outfile,'w') {|out| out.print(string) }
    outfile
  else
    string
  end
end