Class: Validation

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# File 'lib/genevalidator/validation.rb', line 50

def initialize( fasta_filepath, 
                vlist = ["all"], 
                tabular_format = nil, 
                xml_file = nil, 
                raw_seq_file = nil,
                mafft_path = nil, 
                start_idx = 1)
  begin

    @fasta_filepath = fasta_filepath
    @xml_file = xml_file
    @vlist = vlist.map{|v| v.gsub(/^\s/,"").gsub(/\s\Z/,"").split(/\s/)}.flatten
    @idx = 0

    if start_idx == nil
      @start_idx = 1
    else
      @start_idx = start_idx
    end

    raise FileNotFoundException.new unless File.exists?(@fasta_filepath)
    fasta_content = IO.binread(@fasta_filepath);

    # the expected type for the sequences is the
    # type of the first query
     
    # autodetect the type of the sequence in the FASTA
    # also check if the fasta file contains a single type of queries
    @type = BlastUtils.type_of_sequences(fasta_content)

    # create a list of index of the queries in the FASTA
    @query_offset_lst = fasta_content.enum_for(:scan, /(>[^>]+)/).map{ Regexp.last_match.begin(0)}
    @query_offset_lst.push(fasta_content.length)
    fasta_content   = nil # free memory for variable fasta_content
    @tabular_format = tabular_format

    if mafft_path == nil
      @mafft_path = which("mafft")
    else
      @mafft_path = mafft_path
    end

    begin
      # index raw_sequence file
      if raw_seq_file != nil
        raise FileNotFoundException.new unless File.exists?(raw_seq_file)
        # leave only the identifiers in the fasta description
        content = File.open(raw_seq_file, "rb").read
        File.open(raw_seq_file, 'w+') { |file| file.write(content.gsub(/ .*/, ""))}

        #index the fasta file
        keys = content.scan(/>(.*)\n/).flatten
        values = content.enum_for(:scan, /(>[^>]+)/).map{ Regexp.last_match.begin(0)}

        # make am index hash
        index_hash = {}
        index_hash = keys.each_with_index{|k, i| index_hash[keys[i]] = values[i]}
        
        puts index_hash

        # create FASTA index
        @raw_seq_file_index = "#{raw_seq_file}.idx"

      end
      rescue Exception => error
        $stderr.print "Error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
          "Possible cause: your file with raw sequences is not FASTA. Please use get_raw_sequences executable to create a correct one.\n"       
    end
 
    # build the path of html folder output
    path = File.dirname(@fasta_filepath)
    @html_path = "#{fasta_filepath}.html"
    @yaml_path = path

    @filename = File.basename(@fasta_filepath)#.scan(/\/([^\/]+)$/)[0][0]
    @all_query_outputs = []

    # create 'html' directory
    FileUtils.rm_rf(@html_path)
    Dir.mkdir(@html_path)

    # copy auxiliar folders to the html folder
    FileUtils.cp_r("aux/css", @html_path)
    FileUtils.cp_r("aux/js", @html_path)
    FileUtils.cp_r("aux/img", @html_path)
    FileUtils.cp_r("aux/font", @html_path)
    FileUtils.cp_r("aux/doc", @html_path)

  rescue SequenceTypeError => error
    $stderr.print "Sequence Type error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
     "Possible cause: input file containes mixed sequence types.\n"      
    exit 
  rescue FileNotFoundException => error
    $stderr.print "File not found error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}."<<
     "Possible cause: input file does not exist.\n"
    exit 
  end
end

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# File 'lib/genevalidator/validation.rb', line 320

def do_validations(prediction, hits)
  begin
  begin
    hits = remove_identical_hits(prediction, hits)
    rescue Exception => error #NoPIdentError
  end
  
  # do validations
  begin

    query_output                = Output.new(@filename, @html_path, @yaml_path, @idx, @start_idx)
    query_output.prediction_len = prediction.length_protein
    query_output.prediction_def = prediction.definition
    query_output.nr_hits        = hits.length

    plot_path = "#{html_path}/#{filename}_#{@idx}"

    validations = []
    validations.push LengthClusterValidation.new(@type, prediction, hits, plot_path)
    validations.push LengthRankValidation.new(@type, prediction, hits)
    validations.push BlastReadingFrameValidation.new(@type, prediction, hits)
    validations.push GeneMergeValidation.new(@type, prediction, hits, plot_path)
    validations.push DuplicationValidation.new(@type, prediction, hits, @mafft_path, @raw_seq_file_index)
    validations.push OpenReadingFrameValidation.new(@type, prediction, hits, plot_path, ["ATG"])
    validations.push AlignmentValidation.new(@type, prediction, hits, plot_path, @mafft_path, @raw_seq_file_index)

    # check the class type of the elements in the list
    validations.map do |v|
      raise ValidationClassError unless v.is_a? ValidationTest
    end

    # check alias duplication
    unless validations.map{|v| v.cli_name}.length == validations.map{|v| v.cli_name}.uniq.length
      raise AliasDuplicationError 
    end

    if vlist.map{|v| v.strip.downcase}.include? "all"
      validations.map{|v| v.run}
      # check the class type of the validation reports
      validations.each do |v|
        raise ReportClassError unless v.validation_report.is_a? ValidationReport
      end
      query_output.validations = validations
    else
      desired_validations = validations.select {|v| vlist.map{|vv| vv.strip.downcase}.include? v.cli_name.downcase }
      desired_validations.each do |v|
          v.run
          raise ReportClassError unless v.validation_report.is_a? ValidationReport
      end
      query_output.validations = desired_validations
      if query_output.validations.length == 0
        raise NoValidationError
      end
    end

  rescue ValidationClassError => error
    $stderr.print "Class Type error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
      "Possible cause: type of one of the validations is not ValidationTest\n"
    exit!
  rescue NoValidationError => error
    $stderr.print "Validation error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
      "Possible cause: your -v arguments are not valid aliases\n"
    exit!
  rescue ReportClassError => error
    $stderr.print "Class Type error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
      "Possible cause: type of one of the validation reports returned by the 'run' method is not ValidationReport\n"
    exit!
  rescue AliasDuplicationError => error
    $stderr.print "Alias Duplication error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}. "<<
      "Possible cause: At least two validations have the same CLI alias\n"
    exit!
  rescue Exception => error
    $stderr.print "Error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}.\n"
    exit!
  end
 
  query_output.generate_html
  query_output.print_output_console
  query_output.print_output_file_yaml
  @all_query_outputs.push(query_output)
rescue Exception => error
  $stderr.print "Error at #{error.backtrace[0].scan(/\/([^\/]+:\d+):.*/)[0][0]}.\n"
  exit
end

end