Class: GeneValidator::Output

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/genevalidator/output.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(current_idx, no_of_hits, definition) ⇒ Output

Initilizes the object Params: current_idx: index of the current query



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# File 'lib/genevalidator/output.rb', line 24

def initialize(current_idx, no_of_hits, definition)
  @opt             = opt
  @dirs            = dirs
  @config          = config
  @config[:run_no] += 1
  output_dir       = @dirs[:output_dir]
  @output_filename = File.join(output_dir, "#{@dirs[:filename]}_results")

  @prediction_def = definition
  @nr_hits        = no_of_hits
  @idx            = current_idx
end

Instance Attribute Details

#fails ⇒ Object

Returns the value of attribute fails.



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# File 'lib/genevalidator/output.rb', line 17

def fails
  @fails
end

#idx ⇒ Object

Returns the value of attribute idx.



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# File 'lib/genevalidator/output.rb', line 14

def idx
  @idx
end

#nr_hits ⇒ Object

Returns the value of attribute nr_hits.



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# File 'lib/genevalidator/output.rb', line 9

def nr_hits
  @nr_hits
end

#overall_score ⇒ Object

Returns the value of attribute overall_score.



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# File 'lib/genevalidator/output.rb', line 16

def overall_score
  @overall_score
end

#prediction_def ⇒ Object

Returns the value of attribute prediction_def.



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# File 'lib/genevalidator/output.rb', line 8

def prediction_def
  @prediction_def
end

#successes ⇒ Object

Returns the value of attribute successes.



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# File 'lib/genevalidator/output.rb', line 18

def successes
  @successes
end

#validations ⇒ Object

list of ValidationReport objects



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# File 'lib/genevalidator/output.rb', line 12

def validations
  @validations
end

Class Method Details

.calculate_no_quries_with_no_evidence(json_data) ⇒ Object

calculate number of queries that had warnings for all validations.



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# File 'lib/genevalidator/output.rb', line 141

def calculate_no_quries_with_no_evidence(json_data)
  all_warnings = 0
  json_data.each do |row|
    status = row[:validations].map { |_, h| h[:status] }
    if status.count { |r| r == 'warning' } == status.length
      all_warnings += 1
    end
  end
  all_warnings
end

.calculate_run_time(json_data) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 175

def calculate_run_time(json_data)
  run_time = Hash.new(Pair1.new(0, 0))
  json_data.map do |row|
    row[:validations].each do |short_header, v|
      next if v[:run_time].nil? || v[:run_time].zero?
      next if v[:validation] == 'unapplicable' || v[:validation] == 'error'
      p = Pair1.new(run_time[short_header.to_s].x + v[:run_time],
                    run_time[short_header.to_s].y + 1)
      run_time[short_header.to_s] = p
    end
  end
  run_time
end

.count_internet_errors(json_data) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 159

def count_internet_errors(json_data)
  json_data.count do |row|
    num = row[:validations].count { |_, h| h[:print] == 'Internet error' }
    num.zero? ? false : true
  end
end

.count_mafft_errors(json_data) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 152

def count_mafft_errors(json_data)
  json_data.count do |row|
    num = row[:validations].count { |_, h| h[:print] == 'Mafft error' }
    num.zero? ? false : true
  end
end

.generate_evaluation_text(overview) ⇒ Object

Calculates an overall evaluation of the output Params: all_query_outputs: Array of ValidationTest objects Output Array of Strigs with the reports



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# File 'lib/genevalidator/output.rb', line 195

def generate_evaluation_text(overview)
  eval       = general_overview(overview)
  error_eval = errors_overview(overview)
  time_eval  = time_overview(overview)

  [eval, error_eval, time_eval].reject(&:empty?)
end

.generate_overview(json_data, min_blast_hits) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 111

def generate_overview(json_data, min_blast_hits)
  scores_from_json = json_data.map { |e| e[:overall_score] }
  quartiles = scores_from_json.all_quartiles
  nee = calculate_no_quries_with_no_evidence(json_data)
  no_mafft = count_mafft_errors(json_data)
  no_internet = count_internet_errors(json_data)
  map_errors = map_errors(json_data)
  run_time = calculate_run_time(json_data)
  min_hits = json_data.count { |e| e[:no_hits] < min_blast_hits }
  overview_hash(scores_from_json, quartiles, nee, no_mafft, no_internet,
                map_errors, run_time, min_hits)
end

.map_errors(json_data) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 166

def map_errors(json_data)
  errors = Hash.new(0)
  json_data.each do |row|
    e = row[:validations].map { |s, h| s if h[:validation] == 'error' }
    e.compact.each { |err| errors[err] += 1 }
  end
  errors
end

.overview_hash(scores_from_json, quartiles, nee, no_mafft, no_internet, map_errors, run_time, insufficient_BLAST_hits) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 124

def overview_hash(scores_from_json, quartiles, nee, no_mafft, no_internet,
                  map_errors, run_time, insufficient_BLAST_hits)
  {
    scores: scores_from_json,
    no_queries: scores_from_json.length,
    good_scores: scores_from_json.count { |s| s >= 75 },
    bad_scores: scores_from_json.count { |s| s < 75 },
    nee: nee, no_mafft: no_mafft, no_internet: no_internet,
    map_errors: map_errors, run_time: run_time,
    first_quartile_of_scores: quartiles[0],
    second_quartile_of_scores: quartiles[1],
    third_quartile_of_scores: quartiles[2],
    insufficient_BLAST_hits: insufficient_BLAST_hits
  }
end

.print_console_footer(overall_evaluation, opt) ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 103

def print_console_footer(overall_evaluation, opt)
  return unless (opt[:output_formats].include? 'stdout') ||
                opt[:hide_summary]
  warn ''
  warn "==> #{overall_evaluation.join("\n")}"
  warn ''
end

Instance Method Details

#generate_json ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 48

def generate_json
  fname = File.join(@dirs[:json_dir], "#{@dirs[:filename]}_#{@idx}.json")
  row_data = { idx: @idx, overall_score: @overall_score,
               definition: @prediction_def, no_hits: @nr_hits }
  row = create_validation_hash(row_data)
  arr_idx = @idx - 1
  @config[:json_output][arr_idx] = row
  File.open(fname, 'w') { |f| f.write(row.to_json) }
end

#print_output_console ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 37

def print_output_console
  return unless @opt[:output_formats].include? 'stdout'
  c_fmt = "%3s\t%5s\t%20s\t%7s\t"
  mutex.synchronize do
    print_console_header(c_fmt)
    short_def = @prediction_def.split(' ')[0]
    print format(c_fmt, @idx, @overall_score, short_def, @nr_hits)
    puts validations.map(&:print).join("\t").gsub('&nbsp;', ' ')
  end
end