Class: GeneValidator::ORFValidationOutput

Inherits:
ValidationReport show all
Defined in:
lib/genevalidator/validation_open_reading_frame.rb

Overview

Class that stores the validation output information

Instance Attribute Summary collapse

Attributes inherited from ValidationReport

#approach, #conclusion, #description, #errors, #expected, #explanation, #header, #message, #plot_files, #run_time, #short_header, #validation_result

Instance Method Summary collapse

Methods inherited from ValidationReport

#color

Constructor Details

#initialize(short_header, header, description, orfs, coverage, longest_orf_frame, threshold = 80, expected = :yes) ⇒ ORFValidationOutput

Returns a new instance of ORFValidationOutput.



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

def initialize(short_header, header, description, orfs, coverage,
               longest_orf_frame, threshold = 80, expected = :yes)
  @short_header = short_header
  @header = header
  @description = description

  @orfs         = orfs
  @coverage     = coverage
  @threshold    = threshold
  @expected     = expected
  @result       = validation
  @plot_files   = []
  @mainORFFrame = longest_orf_frame
  @approach     = 'We expect the query sequence to encode a single gene,' \
                  ' thus it should contain one main Open Reading Frame' \
                  ' (ORF) that occupies most of the query sequence.' \
                  ' This validation does not require any BLAST hits.'
  @explanation  = " The longest ORF is in frame #{@mainORFFrame}, where" \
                  " it occupies #{@coverage.round}% of the query" \
                  ' sequence.'
  @conclusion   = conclude
end

Instance Attribute Details

#coverage ⇒ Object (readonly)

Returns the value of attribute coverage.



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# File 'lib/genevalidator/validation_open_reading_frame.rb', line 13

def coverage
  @coverage
end

#mainORFFrame ⇒ Object (readonly)

Returns the value of attribute mainORFFrame.



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# File 'lib/genevalidator/validation_open_reading_frame.rb', line 15

def mainORFFrame
  @mainORFFrame
end

#orfs ⇒ Object (readonly)

Returns the value of attribute orfs.



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

def orfs
  @orfs
end

#result ⇒ Object (readonly)

Returns the value of attribute result.



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

def result
  @result
end

#threshold ⇒ Object (readonly)

Returns the value of attribute threshold.



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

def threshold
  @threshold
end

Instance Method Details

#conclude ⇒ Object 



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# File 'lib/genevalidator/validation_open_reading_frame.rb', line 41

def conclude
  if @result == :yes
    'There is no evidence to believe that there is any problem with the' \
    ' ORF of the query sequence.'
  else
    'This only represents a portion of the query sequence. In some cases' \
    ' this indicates that a frame shift exists in the query sequence.'
  end
end

#print ⇒ Object 



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# File 'lib/genevalidator/validation_open_reading_frame.rb', line 51

def print
  @orfs.map { |elem| elem[1].length }.reduce(:+)
  orf_list = ''
  @orfs.map { |elem| orf_list << "#{elem[0]}:#{elem[1]}," }

  "#{@coverage.round}%&nbsp;(frame&nbsp;#{@mainORFFrame})"
end

#validation ⇒ Object 



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# File 'lib/genevalidator/validation_open_reading_frame.rb', line 59

def validation
  @coverage > @threshold ? :yes : :no
end