Class: Qu::Seqcluster::Options

Inherits:
Object
  • Object
show all
Defined in:
lib/qu/seqcluster/options.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(argv) ⇒ Options

Returns a new instance of Options.



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# File 'lib/qu/seqcluster/options.rb', line 26

def initialize(argv)
  @opts = parse_opts(argv)
end

Instance Attribute Details

#opts ⇒ Object (readonly)

Returns the value of attribute opts.



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# File 'lib/qu/seqcluster/options.rb', line 24

def opts
  @opts
end

Instance Method Details

#parse_opts(argv) ⇒ Object 



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# File 'lib/qu/seqcluster/options.rb', line 31

def parse_opts(argv)

  options = Seqcluster::default_options

  OptionParser.new do |opts|
    opts.banner = "#{PROGRAM} [#{VERSION}]: Cluster DNA/RNA based on k-mer algorithm
Usage: #{PROGRAM} -i seq.fasta -k 9 -c 0.9"

    opts.separator ""
    opts.separator "Required options:"
    opts.separator ""

    opts.on('-i', '--in File', String, 'Input sequence file in fasta format.') do |value|
      if File.directory?(value)
        $stderr.puts "Error: #{value} is a direcotry."
        exit
      end

      unless File.exists?(value)
        $stderr.puts "Error: #{value} is not exists."
        exit
      end
      options.in = value
    end

    opts.separator ""
    opts.separator "Optional options:"
    opts.separator ""

    opts.on('-k', '--kvalue Integer', Integer, "K value, default is #{options.kvalue}.") do |value|
      options.kvalue = value
    end

    opts.on("-o", "--out File", String, "Output file name for storing the results, default is screen.") do |value|
      options.out = File.open(value, 'w')
    end

    opts.on('-c', '--cutoff Float', Float, "Cutoff value for the similarity for cluster, default is #{options.cutoff}.") do |value|
      options.cutoff = value
    end

    opts.separator ""
    opts.separator ""

    opts.on("-h", "--help", "Show this message and quit") do
      puts opts
      exit
    end

    opts.on("-v", "--version", "Show version") do
      puts "#{PROGRAM} #{VERSION}"
      exit
    end

    opts.separator ""
    opts.separator "Author: Wubin Qu <[email protected]>"
    opts.separator ""

    begin
      argv = ["-h"] if argv.empty?
      opts.parse!(argv)
    rescue OptionParser::ParseError => e
      $stderr.puts e.message, "\n", opts
      exit
    end

    if options.in.nil?
      $stderr.puts "Error: option -i required."
      exit
    end
  end
  return options
end