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

   1 #
   2 # = lib/soft/tree_puzzle - TreePuzzle  class
   3 #
   4 # Copyright::  Copyright (C) 2009 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: tree_puzzle.rb,v 1.5 2009/10/08 22:44:54 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 TreePuzzle
  17
  18         VERBOSE = false
  19
  20         OUTDIST = 'outdist'
  21         OUTFILE = 'outfile'
  22         VERSION = '5.2'
  23
  24         def initialize
  25             @tree_puzzle_home = Util.get_env_variable_value( ResourceLocations::TREEPUZZLE_HOME_ENV_VARIABLE )
  26             Util.check_file_for_readability( @tree_puzzle_home )
  27         end
  28
  29         def run( alignment_file, model, rate_heterogeneity, number_of_seqs )
  30             Util.check_file_for_readability( alignment_file )
  31
  32             input = alignment_file
  33             input << "\nk\nk"
  34             if number_of_seqs <= 257
  35                 input << "\nk"
  36             end
  37             input << determine_model_option( model )
  38             input << determine_rate_heterogeneity_option( rate_heterogeneity )
  39             input << "\ny\n"
  40
  41             if VERBOSE
  42                 puts @tree_puzzle_home + " " + input
  43             end
  44             IO.popen( @tree_puzzle_home, 'r+' ) do |io|
  45                 io.puts input
  46                 io.close_write
  47                 return io.read
  48             end
  49         end
  50
  51         private
  52
  53         # "Model of substitution" order for DQO TREE-PUZZLE 5.0:
  54         # Auto
  55         # m -> Dayhoff (Dayhoff et al. 1978)
  56         # m -> JTT (Jones et al. 1992)
  57         # m -> mtREV24 (Adachi-Hasegawa 1996)
  58         # m -> BLOSUM62 (Henikoff-Henikoff 92)
  59         # m -> VT (Mueller-Vingron 2000)
  60         # m -> WAG (Whelan-Goldman 2000)
  61         # m -> Auto
  62         def determine_model_option( model )
  63             cmd = nil
  64             if ( model == :pam )
  65                 cmd = "\nm"
  66             elsif ( model == :jtt )
  67                 cmd = "\nm\nm"
  68             elsif ( model == :mtrev24 )
  69                 cmd = "\nm\nm\nm"
  70             elsif ( model == :blosum62 )
  71                 cmd = "\nm\nm\nm\nm"
  72             elsif ( model == :vt )
  73                 cmd = "\nm\nm\nm\nm\nm"
  74             elsif ( model == :wag )
  75                 cmd = "\nm\nm\nm\nm\nm\nm"
  76             elsif ( model == :auto )
  77                 cmd = ""
  78             else
  79                 error_msg = "unknown model"
  80                 raise ArgumentError, error_msg
  81             end
  82             cmd
  83         end
  84
  85
  86         # Model of rate heterogeneity:
  87         #    "8 Gamma distributed rates"
  88         #    "Two rates (1 invariable + 1 variable)"
  89         #    "Mixed (1 invariable + 8 Gamma rates)"
  90         #    otherwise: Uniform rate
  91         def determine_rate_heterogeneity_option( rates )
  92             opt = nil
  93             if ( rates == :gamma8 )
  94                 opt = "\nw"
  95             elsif ( rates == :inv1_var1 )
  96                 opt = "\nw\nw"
  97             elsif ( rates == :inv1_gamma8 )
  98                 opt = "\nw\nw\nw"
  99             elsif ( rates == :uniform )
 100                 opt = ""
 101             else
 102                 error_msg = "unknown rate heterogeneity option"
 103                 raise ArgumentError, error_msg
 104             end
 105             return opt
 106         end
 107
 108     end # class TreePuzzle
 109
 110 end # module Evoruby