Class: ProphetTool

Inherits:
SearchTool show all
Includes:
LibXML
Defined in:
lib/protk/prophet_tool.rb

Instance Attribute Summary

Attributes inherited from Tool

#option_parser, #options

Instance Method Summary collapse

Methods inherited from SearchTool

#current_database, #jobid_from_filename

Methods inherited from Tool

#input_base_path, #jobid_from_filename, #jobid_prefix, #jobid_prefix=, #method_missing, #output_base_path, #run

Constructor Details

#initialize(option_support = {}) ⇒ ProphetTool

Initializes the commandline options



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# File 'lib/protk/prophet_tool.rb', line 20

def initialize(option_support={})
  option_support[:prefix_suffix]=true;
  option_support[:over_write]=true;
  
  super(option_support)

end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Tool

Instance Method Details

#extract_db(file_name) ⇒ Object

Obtain the database name from the given input file



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

def extract_db(file_name)
  reader = XML::Reader.file(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

#extract_engine(file_name) ⇒ Object

Obtain the search engine name from the input file The name of the engine is returned in lowercase and should contain no spaces Names of common engines are searched for and extracted in simplified form if possible



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# File 'lib/protk/prophet_tool.rb', line 67

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

  while(reader.read)
    if ( reader.name == "search_summary" )
      dbnode=reader.expand
      dbvalue=dbnode['search_engine']
      reader.close
      engine_name=dbvalue.gsub(/ /,"_")
      engine_name=engine_name.gsub(/\(/,"")
      engine_name=engine_name.gsub(/\)/,"")
      engine_name=engine_name.gsub(/\!/,"")        
      return engine_name.downcase
    end
  end
end