Class: OMSSAUtil

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/omssa_util.rb

Class Method Summary collapse

Class Method Details

.add_retention_times(mgf_file, pepxml_file, over_write = false, save = false) ⇒ Object

Reads a pepxml file and modifies it to include retention time info. The modified xml doc is returned but not yet saved



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# File 'lib/protk/omssa_util.rb', line 13

def self.add_retention_times(mgf_file,pepxml_file,over_write=false,save=false)
  parser=XML::Parser.file(pepxml_file)
  pepxml_doc=parser.parse
  rt_table=MascotUtil.index_mgf_times(mgf_file)
  
 #   p "Retention time table #{rt_table}"
  
#    queries=pepxml_doc.find('//x:spectrum_query','x:http://regis-web.systemsbiology.net/pepXML')
  queries=pepxml_doc.find('//spectrum_query')    
  i=0
  queries.each do |query|

    atts=query.attributes
    spect=atts["spectrum"]
    spect.chop!.chop! # Remove charge ... presume it isn't greater than 9!
    
    throw "No spectrum found for spectrum_query #{query}" unless ( spect!=nil)
    throw "No retention time found for spectrum #{spect}. Most likely MALDI data was converted without specifying MALDI option." unless (rt_table[spect]!=nil)
    
    if ( queries[i].attributes["retention_time_sec"]!=nil )
      throw "A retention time value is already present" unless over_write
    end


    if ( queries[i].attributes["retention_time_sec"]==nil || over_write)
      queries[i].attributes["retention_time_sec"]=rt_table[spect]       
      p queries[i].attributes["retention_time_sec"] 
    end
    
    
    i=i+1
  end

  if ( save)
    pepxml_doc.save(pepxml_file)
  end

  return pepxml_doc
end