Class: Bioinform::CLI::ConvertMotif

Inherits:
Object
  • Object
show all
Defined in:
lib/bioinform/cli/convert_motif.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.main(argv) ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 136

def self.main(argv)
  self.new.main(argv)
end

Instance Method Details

#arguments ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 11

def arguments
 @arguments ||= []
end

#main(argv) ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 18

def main(argv)
  parse!(argv, filename_format: './{name}.{ext}')
  motif_files = arguments
  motif_files += $stdin.read.shellsplit  unless $stdin.tty?
  if motif_files.empty?
    puts option_parser.help()
    return
  end

  output_motifs = []
  motifs = motif_files.map do |filename|
    input = File.read(filename)
    case options[:model_from]
    when 'pwm'
      MotifModel::PWM.from_string(input)
    when 'pcm'
      MotifModel::PCM.from_string(input)
    when 'ppm'
      MotifModel::PPM.from_string(input)
    else
      raise "Unknown value of model-from parameter: `#{options[:model_from]}`"
    end
  end
  pcm2pwm_converter = ConversionAlgorithms::PCM2PWMConverter.new(pseudocount: :log, background: Background::Uniform)
  pcm2ppm_converter = ConversionAlgorithms::PCM2PPMConverter.new
  ppm2pcm_converter = ConversionAlgorithms::PPM2PCMConverter.new(count: 100)
  motifs.each do |motif|
    begin
      case options[:model_to]
      when 'pwm'
        if MotifModel.acts_as_pcm?(motif)
          output_motifs << pcm2pwm_converter.convert(motif)
        elsif MotifModel.acts_as_ppm?(motif)
          output_motifs << pcm2pwm_converter.convert(ppm2pcm_converter.convert(motif))
        elsif MotifModel.acts_as_pwm?(motif)
          output_motifs << motif
        else
          raise "Can't be here"
        end
      when 'pcm'
        if MotifModel.acts_as_pcm?(motif)
          output_motifs << motif
        elsif MotifModel.acts_as_ppm?(motif)
          output_motifs << ppm2pcm_converter.convert(motif)
        elsif MotifModel.acts_as_pwm?(motif)
          raise 'Not yet implemented'
        else
          raise "Can't be here"
        end
      when 'ppm'
        if MotifModel.acts_as_pcm?(motif)
          output_motifs << pcm2ppm_converter.convert(motif)
        elsif MotifModel.acts_as_ppm?(motif)
          output_motifs << motif
        elsif MotifModel.acts_as_pwm?(motif)
          raise 'Not yet implemented'
        else
          raise "Can't be here"
        end
      else
        raise "Unknown value of model-to parameter: `#{options[:model_to]}`"
      end
    rescue
      $stderr.puts "One can't convert from #{options[:model_from]} data-model to #{options[:model_to]} data-model"
      raise
    end
  end
  puts output_motifs.join("\n\n")
rescue => e
  $stderr.puts "Error! Conversion wasn't performed"
  $stderr.puts e
  $stderr.puts e.backtrace
end

#option_parser ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 92

def option_parser
  @option_parser ||= OptionParser.new do |cli|
    banner = <<-BANNER
      Usage:
        convert_motif [options] <motif-files>...
        ls | convert_motif [options]

      convert_motif - tool for converting motifs from different input formats
                                                 to different output formats.
      It can change both formatting style and motif models.
      Resulting model is sent to stdout (this can be overriden with --save option).
    BANNER

    cli.version = ::Bioinform::VERSION
    cli.summary_indent = ''
    cli.banner = strip_doc(banner)
    cli.separator ""
    cli.separator "Options:"
    cli.on('--parser PARSER', 'Parser for input motif.'){|parser| options[:parser] = parser}
    cli.on('--formatter FORMATTER', 'Formatter for output motif.'){|formatter| options[:formatter] = formatter}
    cli.on('--from MODEL_OF_INPUT', 'Specify motif model of input.',
                                    'It can be overriden by --parser option',
                                    '(when parser implies certain input model)'){|model_from| options[:model_from] = model_from}
    cli.on('--to MODEL_OF_OUTPUT',  'Specify motif model to convert to.',
                                    'It can be overriden by --formatter option',
                                    '(when formatter implies certain output model)'){|model_to| options[:model_to] = model_to}
    cli.on('--algorithm ALGORITHM', 'Conversion algorithm to transform model.'){|conversion_algorithm| options[:conversion_algorithm] = conversion_algorithm}
    cli.on('--save [FILENAME_FORMAT]',  'Save resulting motifs to according files.',
                                        'filename format by default is ' + options[:filename_format],
                                        'one can specify output folder here',
                                        '{name} is a placeholder for motif name',
                                        '{ext} is a placeholder for motif model') {|filename_format| options[:filename_format] = filename_format  if filename_format}
    cli.on('--[no-]force', 'Overwrite existing files.'){|force| options[:force] = force}
    cli.on('--[no-]silent', 'Suppress error messages and notifications.'){|silent| options[:silent] = silent}
  end
end

#options ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 14

def options
  @options ||= {}
end

#parse!(argv, default_options = {}) ⇒ Object 



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# File 'lib/bioinform/cli/convert_motif.rb', line 129

def parse!(argv, default_options = {})
  @options = default_options.dup
  option_parser.parse!(argv)
  @arguments = argv
end