class GeneValidator::MakerQIValidationOutput
Class that stores the validation output information
Public Class Methods
new(short_header, header, description, splice_sites, exons, expected = :yes)
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# File lib/genevalidator/validation_maker_qi.rb, line 11 def initialize(short_header, header, description, splice_sites, exons, expected = :yes) @short_header = short_header @header = header @description = description @splice_sites = splice_sites @exons = exons @expected = expected @result = validation @approach = 'We obtain the fraction of splice sites and exons' \ ' confirmed by EST/RNASeq alignment from the FASTA' \ ' defline for MAKER predicted gene models. RNASeq is' \ ' often best evidence to ascertain the quality of gene' \ ' models' @explanation = explain @conclusion = conclude end
Public Instance Methods
conclude()
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# File lib/genevalidator/validation_maker_qi.rb, line 41 def conclude if @result == :yes 'More than 80% of this gene is confirmed by RNASeq evidence.' \ 'Thus, the MAKER Quality Index suggests that the query sequence is of' \ ' a good quality.' else 'Less than 80% of this gene is confirmed by RNASeq evidence.' \ 'Thus, the MAKER Quality Index suggests that there may be some issues'\ ' with the query seqeunce.' end end
explain()
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# File lib/genevalidator/validation_maker_qi.rb, line 29 def explain if @splice_sites == -100 "#{@exons}% of exons match an EST/mRNA-seq alignment." \ ' No splice sites were identified and as such cannot be confirmed by' \ ' an EST/mRNA-seq alignment.' else "#{@exons}% of exons match an EST/mRNA-seq alignment and" \ " #{@splice_sites}% of splice sites are confirmed by EST/mRNA-seq" \ ' alignment.' end end
print()
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# File lib/genevalidator/validation_maker_qi.rb, line 53 def print "Exons: #{@exons}%;" \ " Splice Sites: #{@splice_sites}%" end
validation()
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# File lib/genevalidator/validation_maker_qi.rb, line 58 def validation @splice_sites > 80 && @exons > 80 ? :yes : :no end