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_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



20
21
22
23
24
25
26
27
28
 
# 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



32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
 
# 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'
	}
	codes[enzyme_name]

end