Module: Bioinform::CLI::PCM2PWM

Extended by:

Helpers

Defined in:

lib/bioinform/cli/pcm2pwm.rb

Class Method Summary

• .main(argv) ⇒ Object

Methods included from Helpers

basename_changed_extension, basename_wo_extension, change_folder_and_extension, name_wo_extension, set_extension, set_folder

Class Method Details

.main(argv) ⇒ Object

# File 'lib/bioinform/cli/pcm2pwm.rb', line 9

def self.main(argv)
  options = {folder: '.', extension: 'pwm'}
  opt_parser = OptionParser.new do |opts|
    opts.banner = "PCM to PWM converter.\n" +
                  "It transforms files with PCMs into files with PWMs.\n" +
                  "Folder for resulting files to save files can be specified.\n" +
                  "Resulting PWM files have the same name as original file but have another extension (.pwm by default).\n" +
                  "When filelist is empty, it's obtained from STDIN.\n" +
                  "One can use it: `ls -b pcm_folder/*.pcm | pcm2pwm` (ls -b option escape spaces in filenames)\n" +
                  "\n" +
                  "Usage:\n" +
                  "  pcm2pwm [options] [<pcm-files>...]"
    opts.version = ::Bioinform::VERSION
    opts.on('-e', '--extension EXT', 'Extension of output files [default: pwm]') do |v|
      options[:extension] = v
    end
    opts.on('-f', '--folder FOLDER', 'Where to save output files') do |v|
      options[:folder] = v
    end
  end

  opt_parser.parse!(argv)
  pcm_files = argv
  folder = options[:folder]
  extension = options[:extension]

  Dir.mkdir(folder)  unless Dir.exist?(folder)
  filelist = (pcm_files.empty?)  ?  $stdin.read.shellsplit  :  pcm_files

  converter = ConversionAlgorithms::PCM2PWMConverter.new()

  filelist.each do |filename|
    input = File.read(filename)
    motif_data = MatrixParser.new.parse(input)
    pcm = MotifModel::PCM.new(motif_data[:matrix]).named(motif_data[:name])
    pwm = converter.convert(pcm)
    File.open(change_folder_and_extension(filename, extension, folder), 'w') do |f|
      f.puts pwm
    end
  end
end