Method: MS::Sequest::Srf::Sqt.commandline

Defined in:

lib/ms/sequest/srf/sqt.rb

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

# File 'lib/ms/sequest/srf/sqt.rb', line 177

def self.commandline(argv, progname=$0)
  opt = {
    :filter => true
  }
  opts = OptionParser.new do |op|
    op.banner = "usage: #{progname} [OPTIONS] <file>.srf ..."
    op.separator "output: <file>.sqt ..."
    op.separator ""
    op.separator "options:"
    op.on("-d", "--db-info", "calculates num aa's and md5sum on db") {|v| opt[:db_info] = v }
    op.on("-p", "--db-path <String>", "If you need to specify the database path") {|v| opt[:new_db_path] = v }
    op.on("-u", "--db-update", "update the sqt file to reflect --db_path") {|v| opt[:db_update] = v }
    op.on("-n", "--no-filter", "by default, pephit must be within peptide_mass_tolerance",  "(defined in sequest.params) to be included.  Turns this off.") { opt[:filter] = false }
    op.on("-o", "--outfiles <first,...>", Array, "Comma list of output filenames") {|v| opt[:outfiles] = v }
    op.on("-r", "--round", "round floating point values reasonably") {|v| opt[:round] = v }
  end
  opts.parse!(argv)

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

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

  argv.each_with_index do |srf_file,i|
    outfile = 
      if opt[:outfiles]
        opt[:outfiles][i]
      else
        base = srf_file.chomp(File.extname(srf_file))
        base + '.sqt'
      end

    srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
    srf.to_sqt(outfile, :db_info => opt[:db_info], :new_db_path => opt[:new_db_path], :update_db_path => opt[:db_update], :round => opt[:round])
  end
end