class ProphetTool

Public Class Methods

new(option_support=[:prefix,:over_write]) click to toggle source

Initializes the commandline options

Calls superclass method SearchTool::new
# 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
xinteract_code_for_enzyme(enzyme_name) click to toggle source

TODO: Deal with multiple enzyme combos

# 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