transpose-dna.rb

#! /usr/bin/env ruby
# Copyright (c) 2007-2010 Michael Specht
# 
# This file is part of Proteomatic.
# 
# Proteomatic is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# Proteomatic is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with Proteomatic.  If not, see <http://www.gnu.org/licenses/>.

require './include/ruby/proteomatic'

class TransposeDna < ProteomaticScript
    def run()
        # convert all characters to upper case
        dna = @param[:nucleotides].upcase
        # remove invalid characters
        dna.gsub!(/[^CGAT]/, '')
        # reverse sequence
        dna.reverse!
        # replace nucleotides
        dna.tr!('ACGT', 'TGCA')
        # output transposed DNA
        puts dna
        File::open(@output[:result], 'w') { |f| f.puts dna } if @output[:result]
    end
end

script = TransposeDna.new