Class: GeneValidator::Validate
- Inherits:
-
Object
- Object
- GeneValidator::Validate
- Extended by:
- Forwardable
- Defined in:
- lib/genevalidator/validation.rb
Overview
Class that runs the validations (Instatiated for each query)
Instance Method Summary collapse
- #check_validations(vals) ⇒ Object
- #check_validations_output(vals) ⇒ Object
- #compute_scores ⇒ Object
- #create_validation_tests(prediction, hits) ⇒ Object
- #generate_run_output ⇒ Object
- #generate_run_overview ⇒ Object
-
#initialize ⇒ Validate
constructor
Initilizes the object Params:
opt
: A hash with the following keys: validations:, blast_tabular_file:, blast_tabular_options:, blast_xml_file:, db:, raw_sequences:, num_threads:, fast:}start_idx
: number of the sequence from the file to start withoverall_evaluation
: boolean variable for printing overall evaluation. -
#length_validation_scores(validations, scores) ⇒ Object
Since there are two length validations, it is necessary to adjust the scores accordingly.
-
#remove_identical_hits(prediction, hits) ⇒ Object
Removes identical hits (100% coverage and >99% identity) Params:
prediction
: Sequence objecthits
: Array ofSequence
objects Output: new array of hitSequence
objects. -
#validate(prediction, hits, current_idx) ⇒ Object
Validate one query and create validation report Params:
prediction
: Sequence objecthits
: Array ofSequence
objectscurrent_idx
: the index number of the query.
Constructor Details
#initialize ⇒ Validate
Initilizes the object Params: opt
: A hash with the following keys: validations:, blast_tabular_file:, blast_tabular_options:, blast_xml_file:, db:, raw_sequences:, num_threads:, fast:} start_idx
: number of the sequence from the file to start with overall_evaluation
: boolean variable for printing overall evaluation
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# File 'lib/genevalidator/validation.rb', line 101 def initialize @opt = opt @config = config @mutex_array = mutex_array @run_output = nil @overview = overview @query_idx = query_idx end |
Instance Method Details
#check_validations(vals) ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 174 def check_validations(vals) # check the class type of the elements in the list vals.each { |v| fail ValidationClassError unless v.is_a? ValidationTest } # check alias duplication aliases = vals.map(&:cli_name) fail AliasDuplicationError unless aliases.length == aliases.uniq.length rescue ValidationClassError => e $stderr.puts e exit 1 rescue AliasDuplicationError => e $stderr.puts e exit 1 end |
#check_validations_output(vals) ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 188 def check_validations_output(vals) fail NoValidationError if @run_output.validations.length == 0 vals.each do |v| fail ReportClassError unless v.validation_report.is_a? ValidationReport end rescue NoValidationError => e $stderr.puts e exit 1 rescue ReportClassError => e $stderr.puts e exit 1 end |
#compute_scores ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 201 def compute_scores validations = @run_output.validations scores = {} scores[:successes] = validations.count { |v| v.result == v.expected } scores[:fails] = validations.count { |v| v.validation != :unapplicable && v.validation != :error && v.result != v.expected } scores = length_validation_scores(validations, scores) @run_output.successes = scores[:successes] @run_output.fails = scores[:fails] total_query = scores[:successes].to_i + scores[:fails] if total_query == 0 @run_output.overall_score = 0 else @run_output.overall_score = (scores[:successes] * 90 / total_query).round end end |
#create_validation_tests(prediction, hits) ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 160 def create_validation_tests(prediction, hits) val = [] val.push LengthClusterValidation.new(prediction, hits) val.push LengthRankValidation.new(prediction, hits) val.push GeneMergeValidation.new(prediction, hits) val.push DuplicationValidation.new(prediction, hits) if @config[:type] == :nucleotide val.push BlastReadingFrameValidation.new(prediction, hits) val.push OpenReadingFrameValidation.new(prediction, hits) end val.push AlignmentValidation.new(prediction, hits) val.select { |v| @opt[:validations].include? v.cli_name.downcase } end |
#generate_run_output ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 238 def generate_run_output @run_output.generate_html @run_output.generate_json @run_output.print_output_console generate_run_overview end |
#generate_run_overview ⇒ Object
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# File 'lib/genevalidator/validation.rb', line 245 def generate_run_overview vals = @run_output.validations no_mafft = 0 no_internet = 0 errors = [] vals.each do |v| unless v.errors.nil? no_mafft += v.errors.count { |e| e == NoMafftInstallationError } no_internet += v.errors.count { |e| e == NoInternetError } end errors.push(v.short_header) if v.validation == :error end no_evidence = vals.count { |v| v.result == :unapplicable || v.result == :warning } == vals.length nee = (no_evidence) ? 1 : 0 good_scores = (@run_output.overall_score >= 75) ? 1 : 0 bad_scores = (@run_output.overall_score >= 75) ? 0 : 1 @mutex_array.synchronize do @overview[:no_queries] += 1 @overview[:scores].push(@run_output.overall_score) @overview[:good_scores] += good_scores @overview[:bad_scores] += bad_scores @overview[:nee] += nee @overview[:no_mafft] += no_mafft @overview[:no_internet] += no_internet errors.each { |err| @overview[:map_errors][err] += 1 } vals.each do |v| next if v.run_time == 0 || v.run_time.nil? next if v.validation == :unapplicable || v.validation == :error p = Pair1.new(@overview[:run_time][v.short_header].x + v.run_time, @overview[:run_time][v.short_header].y + 1) @overview[:run_time][v.short_header] = p end end end |
#length_validation_scores(validations, scores) ⇒ Object
Since there are two length validations, it is necessary to adjust the
scores accordingly
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# File 'lib/genevalidator/validation.rb', line 220 def length_validation_scores(validations, scores) lcv = validations.select { |v| v.class == LengthClusterValidationOutput } lrv = validations.select { |v| v.class == LengthRankValidationOutput } if lcv.length == 1 && lrv.length == 1 score_lcv = (lcv[0].result == lcv[0].expected) score_lrv = (lrv[0].result == lrv[0].expected) if score_lcv == true && score_lrv == true scores[:successes] -= 1 # if both are true: counted as 1 success elsif score_lcv == false && score_lrv == false scores[:fails] -= 1 # if both are false: counted as 1 fail else scores[:successes] -= 0.5 scores[:fails] -= 0.5 end end scores end |
#remove_identical_hits(prediction, hits) ⇒ Object
Removes identical hits (100% coverage and >99% identity) Params: prediction
: Sequence object hits
: Array of Sequence
objects Output: new array of hit Sequence
objects
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# File 'lib/genevalidator/validation.rb', line 136 def remove_identical_hits(prediction, hits) identical_hits = [] hits.each do |hit| low_identity = hit.hsp_list.select { |hsp| hsp.pidentity < 99 } no_data = hit.hsp_list.select { |hsp| hsp.pidentity.nil? } low_identity += no_data # check the coverage coverage = Array.new(prediction.length_protein, 0) hit.hsp_list.each do |hsp| match_to = hsp.match_query_to match_from = hsp.match_query_from len = match_to - match_from + 1 coverage[match_from - 1..match_to - 1] = Array.new(len, 1) end if low_identity.length == 0 && coverage.uniq.length == 1 identical_hits.push(hit) end end identical_hits.each { |hit| hits.delete(hit) } hits end |
#validate(prediction, hits, current_idx) ⇒ Object
Validate one query and create validation report Params: prediction
: Sequence object hits
: Array of Sequence
objects current_idx
: the index number of the query
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# File 'lib/genevalidator/validation.rb', line 116 def validate(prediction, hits, current_idx) hits = remove_identical_hits(prediction, hits) vals = create_validation_tests(prediction, hits) check_validations(vals) vals.each(&:run) @run_output = Output.new(current_idx, hits.length, prediction.definition) @run_output.validations = vals.map(&:validation_report) check_validations_output(vals) compute_scores generate_run_output end |