Class: DuplicationValidation

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# File 'lib/genevalidator/validation_duplication.rb', line 47

def initialize(type, prediction, hits, mafft_path, index_file_name)
  super
  @mafft_path      = mafft_path
  @index_file_name = index_file_name
  @short_header    = "Duplication"
  @header          = "Duplication"
  @description = "Check whether there is a duplicated subsequence in the"<<
  " predicted gene by counting the hsp residue coverag of the prediction,"<<
  " for each hit. Meaning of the output displayed: P-value of the Wilcoxon"<<
  " test which test the distribution of hit average coverage against 1."<<
  " P-values higher than 5% pass the validation test."
  @cli_name        = "dup"

end

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# File 'lib/genevalidator/validation_duplication.rb', line 66

def run(n=10)    
  begin
    raise NotEnoughHitsError unless hits.length >= 5
    raise Exception unless prediction.is_a? Sequence and
                           prediction.raw_sequence != nil and 
                           hits[0].is_a? Sequence 

    start = Time.new
    # get the first n hits
    less_hits = @hits[0..[n-1,@hits.length].min]
    useless_hits = []
    begin
      # get raw sequences for less_hits
      less_hits.map do |hit|
        #get gene by accession number
        if hit.raw_sequence == nil
          #hit.get_sequence_from_index_file(@index_file_name, hit.identifier)
          if hit.type == :protein
            hit.get_sequence_by_accession_no(hit.accession_no, "protein")
          else
            hit.get_sequence_by_accession_no(hit.accession_no, "nucleotide")
          end
          if hit.raw_sequence == ""
            useless_hits.push(hit)
          end
        end
      end
      rescue Exception => error
        raise NoInternetError
    end
    useless_hits.each{|hit| less_hits.delete(hit)}

    if less_hits.length == 0 
      raise NoInternetError
    end

    averages = []

    less_hits.each do |hit|
      coverage = Array.new(hit.length_protein,0)
      hit.hsp_list.each do |hsp|
      # align subsequences from the hit and prediction that match (if it's the case)
        if hsp.hit_alignment != nil and hsp.query_alignment != nil
          hit_alignment   = hsp.hit_alignment
          query_alignment = hsp.query_alignment
        else
          # indexing in blast starts from 1
          hit_local = hit.raw_sequence[hsp.hit_from-1..hsp.hit_to-1]
          query_local = prediction.raw_sequence[hsp.match_query_from-1..hsp.match_query_to-1]

          # in case of nucleotide prediction sequence translate into protein
          # use translate with reading frame 1 because 
          # to/from coordinates of the hsp already correspond to the 
          # reading frame in which the prediction was read to match this hsp 
          if @type == :nucleotide
            s = Bio::Sequence::NA.new(query_local)
            query_local = s.translate
          end

          # local alignment for hit and query
          seqs = [hit_local, query_local]

          begin
            options   = ['--maxiterate', '1000', '--localpair', '--quiet']
            mafft     = Bio::MAFFT.new(@mafft_path, options)
            report    = mafft.query_align(seqs)
            raw_align = report.alignment
            align     = []

            raw_align.each { |s| align.push(s.to_s) }
            hit_alignment   = align[0]
            query_alignment = align[1]
          rescue Exception => error                
            raise NoMafftInstallationError
          end
        end 

        # check multiple coverage

        # for each hsp of the curent hit
        # iterate through the alignment and count the matching residues
        [*(0 .. hit_alignment.length-1)].each do |i|
          residue_hit = hit_alignment[i]
          residue_query = query_alignment[i]
          if residue_hit != ' ' and residue_hit != '+' and residue_hit != '-'
            if residue_hit == residue_query             
              # indexing in blast starts from 1
              idx = i + (hsp.hit_from-1) - hit_alignment[0..i].scan(/-/).length 
                coverage[idx] += 1
              #end
            end
          end
        end
      end
      overlap = coverage.reject{|x| x==0}
      if overlap != []
        averages.push(overlap.inject(:+)/(overlap.length + 0.0)).map{|x| x.round(2)}
      end
    end
  
    # if all hsps match only one time
    if averages.reject{|x| x==1} == []
      @validation_report = DuplicationValidationOutput.new(1)
      @running_time = Time.now - start
      return @validation_report
    end
    
    pval = wilcox_test(averages)

    @validation_report = DuplicationValidationOutput.new(pval)        
    @running_time = Time.now - start
    return @validation_report

  rescue  NotEnoughHitsError => error
    @validation_report = ValidationReport.new("Not enough evidence", :warning)
    return @validation_report
  rescue NoMafftInstallationError
    @validation_report = ValidationReport.new("Mafft error", :error)
    @validation_report.errors.push NoMafftInstallationError                          
    return @validation_report
  rescue NoInternetError
    @validation_report = ValidationReport.new("Internet error", :error)
    @validation_report.errors.push NoInternetError
    return @validation_report
  rescue Exception => error
    puts error.backtrace
    @validation_report.errors.push OtherError
    @validation_report = ValidationReport.new("Unexpected error", :error)
    return @validation_report
  end
end