Class: SearchTool

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

Direct Known Subclasses

ProphetTool, TandemSearchTool

Instance Attribute Summary

Attributes inherited from Tool

#option_parser, #options, #options_defined_by_user

Instance Method Summary collapse

Methods inherited from Tool

#add_boolean_option, #add_value_option, #check_options, #database_info, default_output_path, extension_from_filename, #jobid_prefix, #jobid_prefix=, #method_missing, #run, #supported_options

Constructor Details

#initialize(option_support = []) ⇒ SearchTool

Initializes commandline options common to all search tools. Individual search tools can add their own options, but should use Capital letters to avoid conflicts



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# File 'lib/protk/search_tool.rb', line 21

def initialize(option_support=[])
  super(option_support)

  # if (option_support.include? :database)
  #   add_value_option(:database,"sphuman",['-d', '--database dbname', 'Specify the database to use for this search. Can be a named protk database or the path to a fasta file'])        
  # end
  
  if ( option_support.include? :enzyme )
    add_value_option(:enzyme,"Trypsin",['--enzyme enz', 'Enzyme'])
  end

  if ( option_support.include? :modifications )
    add_value_option(:var_mods,"",['--var-mods vm','Variable modifications. These should be provided in a comma separated list'])
    add_value_option(:fix_mods,"",['--fix-mods fm','Fixed modifications. These should be provided in a comma separated list'])
  end

  if ( option_support.include? :instrument )
    add_value_option(:instrument,"ESI-QUAD-TOF",['--instrument instrument', 'Instrument'])
  end

  if ( option_support.include? :mass_tolerance_units )
    add_value_option(:fragment_tolu,"Da",['--fragment-ion-tol-units tolu', 'Fragment ion mass tolerance units (Da or mmu). Default=Da'])      
    add_value_option(:precursor_tolu,"ppm",['--precursor-ion-tol-units tolu', 'Precursor ion mass tolerance units (ppm or Da). Default=ppm'])
  end

  if ( option_support.include? :mass_tolerance )
    add_value_option(:fragment_tol,0.65,['-f', '--fragment-ion-tol tol', 'Fragment ion mass tolerance (unit dependent). Default=0.65'])
    add_value_option(:precursor_tol,200,['-p','--precursor-ion-tol tol', 'Precursor ion mass tolerance. Default=200'])
  end
  
  if ( option_support.include? :precursor_search_type )
    add_value_option(:precursor_search_type,"monoisotopic",['-a', '--search-type type', 'Use monoisotopic or average precursor masses. (monoisotopic or average)'])
  end

  if ( option_support.include? :strict_monoisotopic_mass )
    add_boolean_option(:strict_monoisotopic_mass,false,['-s', '--strict-monoisotopic-mass', 'Dont allow for misassignment of monoisotopic mass to another isotopic peak'])
  end

  if ( option_support.include? :missed_cleavages )
    add_value_option(:missed_cleavages,2,['-v', '--num-missed-cleavages num', 'Number of missed cleavages allowed'])
  end

  if ( option_support.include? :cleavage_semi )
    add_boolean_option(:cleavage_semi,false,['--cleavage-semi', 'Search for peptides with up to 1 non-enzymatic cleavage site'])
  end

  if ( option_support.include? :respect_precursor_charges )
    add_boolean_option(:respect_precursor_charges,false,['-q', '--respect-charges','Dont respect charges in the input file. Instead impute them by trying various options'])
  end

  if ( option_support.include? :searched_ions )
    add_value_option(:searched_ions,"",['--searched-ions si', 'Ion series to search (default=b,y)'])
  end

  if ( option_support.include? :multi_isotope_search )
    add_boolean_option(:multi_isotope_search,false,["--multi-isotope-search","Expand parent mass window to include windows around neighbouring isotopic peaks"])
  end

  if ( option_support.include? :num_peaks_for_multi_isotope_search )
    add_value_option(:num_peaks_for_multi_isotope_search,0,["--num-peaks-for-multi-isotope-search np","Number of peaks to include in multi-isotope search"])
  end

  if ( option_support.include? :glyco)
    add_boolean_option(:glyco,false,['-g','--glyco', 'Expect N-Glycosylation modifications as variable mod in a search or as a parameter when building statistical models'])
  end

  if ( option_support.include? :acetyl_nterm)
    add_boolean_option(:acetyl_nterm,false,['-y','--acetyl-nterm', 'Expect N-terminal acetylation as a variable mod in a search or as a parameter when building statistical models'])
  end

  if ( option_support.include? :methionine_oxidation)
    add_boolean_option(:methionine_oxidation,false,['-m', '--methionineo', 'Expect Oxidised Methionine modifications as variable mod in a search'])
  end

  if ( option_support.include? :carbamidomethyl)
    add_boolean_option(:carbamidomethyl,false,['-c', '--carbamidomethyl', 'Expect Carbamidomethyl C modifications as fixed mod in a search'])
  end
  
  if ( option_support.include? :maldi)
    add_boolean_option(:maldi,false,['-l', '--maldi', 'Run a search on MALDI data'])
  end

  @option_parser.summary_width=40

    
end

Dynamic Method Handling

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