Class: TandemSearchTool

Inherits:
SearchTool show all
Defined in:
lib/protk/tandem_search_tool.rb

Instance Attribute Summary collapse

Attributes inherited from Tool

#option_parser, #options, #options_defined_by_user

Instance Method Summary collapse

Methods inherited from Tool

#add_boolean_option, #add_default_to_help, #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 ⇒ 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

Dynamic Method Handling

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

Instance Attribute Details

#default_data_path ⇒ Object (readonly)

Returns the value of attribute default_data_path.



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

def default_data_path
  @default_data_path
end

#defaults_path ⇒ Object (readonly)

Returns the value of attribute defaults_path.



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# File 'lib/protk/tandem_search_tool.rb', line 18

def defaults_path
  @defaults_path
end

#supported_xtandem_keys ⇒ Object (readonly)

Returns the value of attribute supported_xtandem_keys.



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# File 'lib/protk/tandem_search_tool.rb', line 22

def supported_xtandem_keys
  @supported_xtandem_keys
end

#taxonomy_path ⇒ Object (readonly)

Returns the value of attribute taxonomy_path.



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# File 'lib/protk/tandem_search_tool.rb', line 19

def taxonomy_path
  @taxonomy_path
end

Instance Method Details

#params_doc(db_info, taxo_path, input_path, output_path) ⇒ Object 



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# File 'lib/protk/tandem_search_tool.rb', line 236

def params_doc(db_info,taxo_path,input_path,output_path)
    params_parser=XML::Parser.file(@defaults_path)
    std_params=params_parser.parse

    
    throw "Invalid input db_info must be a FastaDatabase object" unless db_info.class==FastaDatabase

  generate_parameter_doc(std_params,output_path,input_path,db_info,taxo_path)
end

#taxonomy_doc(db_info) ⇒ Object 



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# File 'lib/protk/tandem_search_tool.rb', line 215

def taxonomy_doc(db_info)
  throw "Invalid input db_info must be a FastaDatabase object" unless db_info.class==FastaDatabase
  database_path=db_info.path
  taxon=db_info.name
  # Parse taxonomy template file
  #
  taxo_parser=XML::Parser.file(@taxonomy_path)
  taxo_doc=taxo_parser.parse

  taxon_label=taxo_doc.find('/bioml/taxon')
  throw "Exactly one taxon label is required in the taxonomy_template file" unless taxon_label.length==1
  taxon_label[0].attributes['label']=taxon

  db_file=taxo_doc.find('/bioml/taxon/file')
  throw "Exactly one database file is required in the taxonomy_template file" unless db_file.length==1
  db_file[0].attributes['URL']=database_path

  taxo_doc
end