forester/ruby/evoruby/lib/evo/soft/raxml.rb

   1 #
   2 # = lib/soft/raxml - Raxml class
   3 #
   4 # Copyright::  Copyright (C) 2009 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: raxml.rb,v 1.1 2009/10/07 00:08:35 cmzmasek Exp $
   8 #
   9 # last modified: 2009/10/06
  10
  11 require 'lib/evo/soft/resource_locations'
  12 require 'lib/evo/util/util'
  13
  14 module Evoruby
  15
  16     class Raxml
  17
  18         VERBOSE = true
  19
  20         def initialize
  21             @fast_me_home = Util.get_env_variable_value( ResourceLocations::FASTME_HOME_ENV_VARIABLE )
  22             Util.check_file_for_readability( @fast_me_home )
  23         end
  24
  25         def run( pwd_file, bootstrap_number, initial_tree )
  26             Util.check_file_for_readability( pwd_file )
  27             if bootstrap_number == nil || bootstrap_number < 0
  28                 error_msg = "illegal bootstrap number: " + bootstrap_number
  29                 raise ArgumentError, error_msg
  30             end
  31             if initial_tree == nil || (!initial_tree.eql?( "BME" ) && !initial_tree.eql?( "GME" ) && !initial_tree.eql?( "NJ" ) )
  32                 error_msg = "illegal initial tree: " + initial_tree
  33                 raise ArgumentError, error_msg
  34             end
  35             input = String.new()
  36             if bootstrap_number > 1
  37                 input = '-b #{initial_tree} -i #{pwd_file} -n #{bootstrap_number} -s b'
  38             else
  39                 input = '-b #{initial_tree} -i #{pwd_file} -s b'
  40             end
  41             if VERBOSE
  42                 puts @fast_me_home + " " + input
  43             end
  44             IO.popen( @fast_me_home, 'r+' ) do |io|
  45                 io.puts input
  46                 io.close_write
  47                 return io.read
  48             end
  49         end
  50     end # class Raxml
  51
  52 end # module Evoruby