Class: 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, #running_time, #short_header, #type, #validation_report

Instance Method Summary (collapse)

Constructor Details

- (BlastReadingFrameValidation) initialize(type, prediction, hits = nil)

Returns a new instance of BlastReadingFrameValidation



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# File 'lib/genevalidator/validation_blast_reading_frame.rb', line 53

def initialize(type, prediction, hits = nil)
  super
  @short_header = "Frame"
  @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."<<
  " Meaning of the output displayed: (reading frame: no hsps)"
  @cli_name     = "frame"
end

Instance Method Details

- (Object) run(lst = @hits)

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 69

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

    raise NotEnoughHitsError unless hits.length >= 5
    raise Exception unless prediction.is_a? Sequence and hits[0].is_a? Sequence

    start = Time.now

    rfs =  lst.map{ |x| x.hsp_list.map{ |y| y.query_reading_frame}}.flatten
    frames_histo = Hash[rfs.group_by { |x| x }.map { |k, vs| [k, vs.length] }]

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

    @validation_report = BlastRFValidationOutput.new(frames_histo)
    @running_time = Time.now - start
    return @validation_report

  # Exception is raised when blast founds no hits
  rescue  NotEnoughHitsError => error
    @validation_report = ValidationReport.new("Not enough evidence", :warning)
    return @validation_report
  rescue Exception => error
    @validation_report = ValidationReport.new("Unexpected error", :error)
    return @validation_report
  end
end