Method: MS::Sequest::Srf::Search.commandline

Defined in:
lib/ms/sequest/srf/search.rb

.commandline(argv, progname = $0) ⇒ Object 



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# File 'lib/ms/sequest/srf/search.rb', line 112

def self.commandline(argv, progname=$0)
  opt = {
    :format => 'mgf'
  }
  opts = OptionParser.new do |op|
    op.banner = "usage: #{File.basename(__FILE__)} <file>.srf ..."
    op.separator "outputs: <file>.mgf ..."
    op.on("-f", "--format <mgf|dta>", "the output format (default: #{opt[:format]})") {|v| opt[:format] = v }
    op.on("-o", "--outfiles <String,...>", Array, "comma list of output files or directories") {|v| opt[:outfiles] = v }
  end

  opts.parse!(argv)

  if argv.size == 0
    puts(opts) || exit
  end

  format = opt[:format]

  if opt[:outfiles] && (opt[:outfiles].size != argv.size)
    raise "if outfiles specified, needs the same number of files as input files"
  end

  argv.each_with_index do |srf_file,i|
    base = srf_file.chomp(File.extname(srf_file))
    newfile = 
      if opt[:outfiles]
        opt[:outfiles][i]
      else
        case format
        when 'dta'
          base
        when 'mgf'
          base << '.' << format
        end
      end
    srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
    # options just speed up reading since we don't need .out info anyway
    case format
    when 'mgf'
      srf.to_mgf(newfile)
    when 'dta'
      srf.to_dta(newfile)
    end
  end
end