Class: GeneValidator::BlastReadingFrameValidation

Inherits:
ValidationTest show all
Defined in:
lib/genevalidator/validation_blast_reading_frame.rb

Overview

This class contains the methods necessary for reading frame validation based on BLAST output

Instance Attribute Summary

Attributes inherited from ValidationTest

#cli_name, #description, #header, #hits, #prediction, #run_time, #short_header, #type, #validation_report

Instance Method Summary collapse

Constructor Details

#initialize(type, prediction, hits = nil) ⇒ BlastReadingFrameValidation 



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# File 'lib/genevalidator/validation_blast_reading_frame.rb', line 81

def initialize(type, prediction, hits = nil)
  super
  @short_header = 'ReadingFrame'
  @header       = 'Reading Frame'
  @description  = 'Check whether there is a single reading frame among' \
                  ' BLAST hits. Otherwise there might be a reading frame' \
                  ' shift in the query sequence.'
  @cli_name     = 'frame'
end

Instance Method Details

#run(lst = @hits) ⇒ Object

Check reading frame inconsistency Params: lst: vector of Sequence objects Output: BlastRFValidationOutput object



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# File 'lib/genevalidator/validation_blast_reading_frame.rb', line 97

def run(lst = @hits)
  if type.to_s != 'nucleotide'
    @validation_report = ValidationReport.new('', :unapplicable)
    return @validation_report
  end

  fail NotEnoughHitsError unless hits.length >= 5
  fail Exception unless prediction.is_a?(Sequence) && hits[0].is_a?(Sequence)

  start = Time.now

  rfs =  lst.map { |x| x.hsp_list.map(&:query_reading_frame) }.flatten
  frames = Hash[rfs.group_by { |x| x }.map { |k, vs| [k, vs.length] }]

  # get the main reading frame
  main_rf = frames.map { |_k, v| v }.max
  @prediction.nucleotide_rf = frames.select { |_k, v| v == main_rf }.first.first

  @validation_report = BlastRFValidationOutput.new(@short_header, @header,
                                                   @description, frames)
  @validation_report.run_time = Time.now - start
  @validation_report

rescue NotEnoughHitsError
  @validation_report =  ValidationReport.new('Not enough evidence',
                                             :warning, @short_header,
                                             @header, @description)
rescue Exception
  @validation_report = ValidationReport.new('Unexpected error', :error,
                                            @short_header, @header,
                                            @description)
  @validation_report.errors.push 'Unexpected Error'
end