Method: TandemSearchTool#initialize

Defined in:
lib/protk/tandem_search_tool.rb

#initialize ⇒ TandemSearchTool

Returns a new instance of TandemSearchTool.



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# File 'lib/protk/tandem_search_tool.rb', line 24

def initialize

  super([
    :database,
    :explicit_output,
    :over_write,
    :enzyme,
    :modifications,
    :mass_tolerance_units,
    :mass_tolerance,
    :multi_isotope_search,
    :missed_cleavages,
    :cleavage_semi,
    :methionine_oxidation,
    :glyco,
    :acetyl_nterm,
    :threads
      ])

  @xtandem_keys_with_single_multiplicity = {
    :fragment_tol => "spectrum, fragment monoisotopic mass error",
    :missed_cleavages => "scoring, maximum missed cleavage sites",
    :cleavage_semi => "protein, cleavage semi",
    :precursor_tolu => "spectrum, parent monoisotopic mass error units",
    :multi_isotope_search => "spectrum, parent monoisotopic mass isotope error",
    :fragment_tolu => "spectrum, fragment monoisotopic mass error units",
    :acetyl_nterm => "protein, quick acetyl",
    :output_spectra => "output, spectra",
    :threads => "spectrum, threads",
    :enzyme => "protein, cleavage site"
  }

  @xtandem_keys_for_precursor_tol = {
    :precursor_tol => ["spectrum, parent monoisotopic mass error minus", "spectrum, parent monoisotopic mass error plus"]
  }

  @defaults_path="#{File.dirname(__FILE__)}/data/tandem_params.xml"
  @taxonomy_path="#{File.dirname(__FILE__)}/data/taxonomy_template.xml"
  @default_data_path="#{File.dirname(__FILE__)}/data/"
  
  @option_parser.banner = "Run an X!Tandem msms search on a set of mzML input files.\n\nUsage: tandem_search.rb [options] file1.mzML file2.mzML ..."
  @options.output_suffix="_tandem"
  @options.enzyme="[RK]|{P}"
  add_value_option(:tandem_params,"isb_native",['-T', '--tandem-params tandem', 'Either the full path to an xml file containing a complete set of default parameters, or one of the following (isb_native,isb_kscore,gpm). Default is isb_native'])
  add_boolean_option(:keep_params_files,false,['-K', '--keep-params-files', 'Keep X!Tandem parameter files'])
  add_boolean_option(:output_spectra,false,['--output-spectra', 'Include spectra in the output file'])

end