Module: Macroape::CLI::Helper

Defined in:
lib/macroape/cli.rb

Class Method Summary collapse

Class Method Details

.find_pvalue_info_string(data, parameters) ⇒ Object 



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# File 'lib/macroape/cli.rb', line 179

def self.find_pvalue_info_string(data, parameters)
  OutputInformation.new(data) {|infos|
    infos.add_parameter('V', 'discretization value', parameters[:discretization])
    infos.background_parameter('B', 'background', parameters[:background])

    infos.add_table_parameter('T', 'threshold', :threshold)
    infos.add_table_parameter('W', 'number of recognized words', :number_of_recognized_words)  if parameters[:background].wordwise?
    infos.add_table_parameter('P', 'P-value', :pvalue)
  }.result
end

.scan_collection_infos_string(data, parameters) ⇒ Object 



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# File 'lib/macroape/cli.rb', line 151

def self.scan_collection_infos_string(data, parameters)
  OutputInformation.new(data) { |infos|
    infos.add_parameter('MS', 'minimal similarity to output', parameters[:cutoff])
    infos.add_parameter('P', 'P-value', parameters[:pvalue])
    infos.add_parameter('PB', 'P-value boundary', parameters[:pvalue_boundary])
    if parameters[:precision_mode] == :precise
      infos.add_parameter('VR', 'discretization value, rough', parameters[:rough_discretization])
      infos.add_parameter('VP', 'discretization value, precise', parameters[:precise_discretization])
      infos.add_parameter('MP', 'minimal similarity for the 2nd pass in \'precise\' mode', parameters[:minimal_similarity])
    else
      infos.add_parameter('V', 'discretization value', parameters[:rough_discretization])
    end
    infos.background_parameter('BQ', 'background for query matrix', parameters[:query_background])
    infos.background_parameter('BC', 'background for collection', parameters[:collection_background])

    infos.add_table_parameter_without_description('motif', :name)
    infos.add_table_parameter_without_description('similarity', :similarity)
    infos.add_table_parameter_without_description('shift', :shift)
    infos.add_table_parameter_without_description('overlap', :overlap)
    infos.add_table_parameter_without_description('orientation', :orientation)
    if parameters[:precision_mode] == :precise
      infos.add_table_parameter_without_description('precise mode', :precision_mode){|precision| precision == :precise ? '*' : '.' }
    end
  }.result
end

.similarity_info_string(info) ⇒ Object 



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# File 'lib/macroape/cli.rb', line 103

def self.similarity_info_string(info)
  OutputInformation.new { |infos|
    infos.add_parameter('V', 'discretization', info[:discretization] )
    infos.add_parameter('P', 'requested P-value', info[:requested_pvalue])  unless info[:predefined_threshold_first] && info[:predefined_threshold_second]
    infos.add_parameter('T1', 'threshold for the 1st matrix', info[:predefined_threshold_first] )  if info[:predefined_threshold_first]
    infos.add_parameter('T2', 'threshold for the 2nd matrix', info[:predefined_threshold_second] )  if info[:predefined_threshold_second]
    infos.add_parameter('PB', 'P-value boundary', info[:pvalue_boundary])
    if info[:first_background] == info[:second_background]
      infos.background_parameter('B', 'background', info[:first_background])
    else
      infos.background_parameter('B1', 'background for the 1st model', info[:first_background])
      infos.background_parameter('B2', 'background for the 2nd model', info[:second_background])
    end

    infos.add_resulting_value('S', 'similarity', info[:similarity])
    infos.add_resulting_value('D', 'distance (1-similarity)', info[:tanimoto])
    infos.add_resulting_value('L', 'length of the alignment', info[:alignment_length])
    infos.add_resulting_value('SH', 'shift of the 2nd PWM relative to the 1st', info[:shift])
    infos.add_resulting_value('OR', 'orientation of the 2nd PWM relative to the 1st', info[:orientation])
    infos.add_resulting_value('A1', 'aligned 1st matrix', info[:text].lines.to_a.first.strip )
    infos.add_resulting_value('A2', 'aligned 2nd matrix', info[:text].lines.to_a.last.strip )
    infos.add_resulting_value('W', 'number of words recognized by both models (model = PWM + threshold)', info[:recognized_by_both] )
    infos.add_resulting_value('W1', 'number of words and recognized by the first model', info[:recognized_by_first] )
    infos.add_resulting_value('P1', 'P-value for the 1st matrix', info[:real_pvalue_first] )
    infos.add_resulting_value('T1', 'threshold for the 1st matrix', info[:threshold_first] )  unless info[:predefined_threshold_first]
    infos.add_resulting_value('W2', 'number of words recognized by the 2nd model', info[:recognized_by_second] )
    infos.add_resulting_value('P2', 'P-value for the 2nd matrix', info[:real_pvalue_second] )
    infos.add_resulting_value('T2', 'threshold for the 2nd matrix', info[:threshold_second] )  unless info[:predefined_threshold_second]
  }.result
end

.threshold_infos_string(data, parameters) ⇒ Object 



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# File 'lib/macroape/cli.rb', line 136

def self.threshold_infos_string(data, parameters)
  OutputInformation.new(data) { |infos|
    infos.add_parameter('V', 'discretization value', parameters[:discretization])
    infos.add_parameter('PB', 'P-value boundary', parameters[:pvalue_boundary])
    infos.background_parameter('B', 'background', parameters[:background])

    infos.add_table_parameter('P', 'requested P-value', :expected_pvalue)
    infos.add_table_parameter('AP', 'actual P-value', :real_pvalue)
    infos.add_table_parameter('W', 'number of recognized words', :recognized_words)  if parameters[:background].wordwise?
    infos.add_table_parameter('T', 'threshold', :threshold)
  }.result
end