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, #options_defined_by_user

Class Method Summary collapse

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(option_support = [:prefix,:over_write]) ⇒ ProphetTool

Initializes the commandline options



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

def initialize(option_support=[:prefix,:over_write])
  
  super(option_support)

  if ( option_support.include? :probability_threshold )
    add_value_option(:probability_threshold,0.05,['--p-thresh val', 'Probability threshold below which PSMs are discarded'])
  end

end

Dynamic Method Handling

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

Class Method Details

.xinteract_code_for_enzyme(enzyme_name) ⇒ Object

TODO: Deal with multiple enzyme combos



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

def self.xinteract_code_for_enzyme(enzyme_name)

  codes = {
    'trypsin' => 'T',
    'stricttrypsin' => 'S',
    'chymotrypsin' => 'C',
    'ralphtrypsin' => 'R',
    'aspn' => 'A',
    'gluc' => 'G',
    'glucbicarb' => 'B',
    'cnbr' => 'M',
    'elastase' => 'E',
    'lysn' => 'L',
    'nonspecific' => 'N',
    'no enzyme' => 'N',
    'unspecific cleavage' => 'N'
  }
  codes[enzyme_name]

end