Class: GeneValidator::MakerQIValidation

Inherits:
ValidationTest show all
Defined in:
lib/genevalidator/validation_maker_qi.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) ⇒ MakerQIValidation

Returns a new instance of MakerQIValidation.



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# File 'lib/genevalidator/validation_maker_qi.rb', line 67

def initialize(type, prediction, hits = nil)
  super
  @short_header = 'QualityIndex'
  @header       = 'Quality Index'
  @description  = 'MAKER mRNA Quality Index'
  @cli_name     = 'maker_qi'
end

Instance Method Details

#run ⇒ Object

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



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

def run
  raise unless prediction.is_a?(Query)

  start  = Time.now

  number = '-?\d*\.?\d*'
  match  = @prediction.definition.match(/QI:#{number}\|(#{number})\|
                                         (#{number})\|#{number}\|
                                         #{number}\|#{number}\|#{number}\|
                                         #{number}\|#{number}/x)

  raise NotEnoughEvidence if match.nil?

  # % of splice sites confirmed by EST/mRNA-seq alignment
  splice_sites = (match[1].to_f * 100).round
  # % of exons that match an EST/mRNA-seq alignment
  exons = (match[2].to_f * 100).round

  @validation_report = MakerQIValidationOutput.new(@short_header, @header,
                                                   @description,
                                                   splice_sites, exons)
  @validation_report.run_time = Time.now - start
  @validation_report
rescue NotEnoughEvidence
  @validation_report = ValidationReport.new('No MAKER Quality Index',
                                            :warning, @short_header,
                                            @header, @description)
rescue StandardError
  @validation_report = ValidationReport.new('Unexpected error', :error,
                                            @short_header, @header,
                                            @description)
  @validation_report.errors.push 'Unexpected Error'
end