Method: PepXML#extract_db

Defined in:
lib/protk/pepxml.rb

#extract_db ⇒ Object

Obtain the database name from the given input file



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# File 'lib/protk/pepxml.rb', line 32

def extract_db()
  reader = XML::Reader.file(self.file_name)
  throw "Failed to open xml file #{file_name}" unless reader!=nil

  while(reader.read)
    # For pep.xml files
    #
    if ( reader.name == "search_database" )
      dbnode=reader.expand
      dbvalue=dbnode['local_path']
      reader.close
      return dbvalue
    end

    # For prot.xml files
    #
    if ( reader.name == "protein_summary_header" )
      dbnode=reader.expand
      dbvalue=dbnode['reference_database']
      reader.close
      return dbvalue
    end
    
    
    
  end

end