class ProphetTool
Public Class Methods
new(option_support=[:prefix,:over_write])
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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)
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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