#
# = lib/evo/apps/taxonomy_processor - TaxonomyProcessor class
#
# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
# License:: GNU Lesser General Public License (LGPL)
#
# $Id: taxonomy_processor.rb,v 1.26 2010/12/13 19:00:11 cmzmasek Exp $
require 'lib/evo/util/util'
require 'lib/evo/msa/msa_factory'
require 'lib/evo/msa/msa'
require 'lib/evo/io/msa_io'
require 'lib/evo/io/parser/fasta_parser'
require 'lib/evo/io/parser/general_msa_parser'
require 'lib/evo/io/writer/fasta_writer'
require 'lib/evo/io/writer/phylip_sequential_writer'
require 'lib/evo/util/command_line_arguments'
module Evoruby
class TaxonomyProcessor
PRG_NAME = "tap"
PRG_DATE = "2010.02.24"
PRG_DESC = "replacement of species names in multiple sequence files"
PRG_VERSION = "1.01"
COPYRIGHT = "2010 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
WWW = "www.phylosoft.org"
EXTRACT_TAXONOMY_OPTION = "t"
def initialize()
@taxonomies = Hash.new()
end
def run()
Util.print_program_information( PRG_NAME,
PRG_VERSION,
PRG_DESC,
PRG_DATE,
COPYRIGHT,
CONTACT,
WWW,
STDOUT )
if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 && ARGV.length != 5 && ARGV.length != 6 ) )
puts( "Usage: #{PRG_NAME}.rb [options] [input map file]