wurmlab/GeneValidator

require 'forwardable'

require 'genevalidator/exceptions'
require 'genevalidator/validation_report'
require 'genevalidator/validation_test'

module GeneValidator
  ##
  # Class that stores the validation output information
  class BlastRFValidationOutput < ValidationReport
    attr_reader :frames
    attr_reader :msg
    attr_reader :total_hsp
    attr_reader :result

    def initialize(short_header, header, description, frames,
                   expected = :yes)
      @short_header = short_header
      @header = header
      @description = description
      @frames = frames
      @expected     = expected
      @result       = validation

      @msg          = ''
      @exp_msg      = ''
      @total_hsp    = 0
      @frames.each do |x, y|
        @msg << "#{y}&nbsp;HSPs&nbsp;align&nbsp;in&nbsp;frame&nbsp;#{x}; "
        @exp_msg << "#{y} HSPs align in frame #{x}; "
        @total_hsp += y.to_i
      end

      @approach     = 'We expect the query sequence to encode a single gene,' \
                      ' thus it should contain one main Open Reading Frame' \
                      ' (ORF). All BLAST hits are thus expected to align' \
                      ' within this ORF.'
      @explanation  = explain
      @conclusion   = conclude
    end

    def explain
      t = "BLAST identified #{@total_hsp} High-scoring Segment Pairs" \
             ' (HSPs)'
      if @result == :yes # i.e. if there is only one ORF...
        frame = @frames.keys[0].to_s
        t1    = "; all of these align in frame #{frame}."
      else
        t1 = ": #{@exp_msg.gsub(/; $/, '')}."
      end
      t + t1
    end

    def conclude
      if @result == :yes # i.e. if there is only one ORF...
        'This is as expected.'
      else
        'The HSPs align in mulitple reading frames, this suggests there may' \
        ' be a frame shift in the query sequence.'
      end
    end

    def print
      @msg.gsub(/; $/, '')
    end

    def validation
      # chack if there are different reading frames
      count_p = 0
      count_n = 0
      frames.each do |x, _y|
        count_p += 1 if x > 0
        count_n += 1 if x < 0
      end
      count_p > 1 || count_n > 1 ? :no : :yes
    end
  end

  ##
  # This class contains the methods necessary for
  # reading frame validation based on BLAST output
  class BlastReadingFrameValidation < ValidationTest
    extend Forwardable
    def_delegators GeneValidator, :opt

    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

    ##
    # Check reading frame inconsistency
    # Params:
    # +lst+: vector of +Sequence+ objects
    # Output:
    # +BlastRFValidationOutput+ object
    def run(lst = @hits)
      if type.to_s != 'nucleotide'
        @validation_report = ValidationReport.new('', :unapplicable)
        return @validation_report
      end

      raise NotEnoughHitsError if hits.length < opt[:min_blast_hits]
      raise unless prediction.is_a?(Query) && hits[0].is_a?(Query)

      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.find { |_k, v| v == main_rf }.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 StandardError
      @validation_report = ValidationReport.new('Unexpected error', :error,
                                                @short_header, @header,
                                                @description)
      @validation_report.errors.push 'Unexpected Error'
    end
  end
end