binaries/src/mafft/core/newick2mafft.rb

   1 #! /usr/bin/env ruby
   2
   3 #version 2, 2009/01/24
   4
   5
   6 if ARGV.length == 1
   7         scale = 1.0
   8 elsif ARGV.length == 2
   9         scale = ARGV.shift.to_f
  10 else
  11         STDERR.puts "USAGE: newick2mafft.rb scale input_tree > output"
  12         exit
  13 end
  14
  15 if scale <= 0.0 then
  16         STDERR.puts "Inappropriate scale, #{scale.to_s}"
  17         exit
  18 end
  19
  20 STDERR.puts "scale = " + scale.to_s
  21
  22 infp = File.open( ARGV.shift, "r" )
  23
  24 tree = ""
  25 while line = infp.gets
  26         tree += line.strip
  27         break if tree =~ /;$/
  28 end
  29 infp.close
  30
  31
  32 #tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "").gsub(/:\-[0-9\.]+/, ":0.0" )
  33 tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "")
  34
  35
  36 STDERR.puts "Initial tree = " +  tree
  37
  38 def resolve( tree )
  39
  40
  41 while 1
  42 #       p tree
  43         tree.sub!( /\,([0-9]+):(\-?[0-9\.]+)\,([0-9]+):(\-?[0-9\.]+)/, ",XXX" )
  44         hit1 = $1
  45         hit2 = $2
  46         hit3 = $3
  47         hit4 = $4
  48
  49 #       p hit1
  50 #       p hit2
  51 #       p hit3
  52 #       p hit4
  53
  54 #       puts "introduce XXX"
  55 #       p tree
  56
  57         break unless tree.index(/XXX/)
  58
  59         poshit = tree.index(/XXX/)
  60 #       puts "poshit=" + poshit.to_s
  61
  62         i = poshit
  63         height = 0
  64         while i >= 0
  65                 break if height == 0 && tree[i..i] == '('
  66                 if tree[i..i] == ')' then
  67                         height += 1
  68                 elsif tree[i..i] == '(' then
  69                         height -= 1
  70                 end
  71                 i -= 1
  72         end
  73
  74         poskakko = i
  75 #       puts "poskakko = " + poskakko.to_s
  76         zenhan = tree[0..poskakko]
  77         zenhan = "" if poskakko == -1
  78 #       puts "zenhan = " + zenhan
  79
  80         treelen = tree.length
  81         tree = zenhan + "(" + tree[poskakko+1..treelen]
  82 #       puts "add ("
  83 #       p tree
  84         tree.sub!( /XXX/, "#{hit1}:#{hit2}):0,#{hit3}:#{hit4}" )
  85
  86 #       p tree
  87 end
  88
  89
  90 return tree
  91
  92 end
  93
  94 memi = [-1,-1]
  95 leni = [-1,-1]
  96
  97 while tree.index( /\(/ )
  98
  99         tree = resolve( tree )
 100
 101         tree.sub!( /\(([0-9]+):(\-?[0-9\.]+),([0-9]+):(\-?[0-9\.]+)\)/, "XXX" )
 102         memi[0] = $1.to_i
 103         leni[0] = $2.to_f * scale
 104         memi[1] = $3.to_i
 105         leni[1] = $4.to_f * scale
 106
 107         if leni[0] > 10 || leni[1] > 10 then
 108                 STDERR.puts ""
 109                 STDERR.puts "Please check the scale of branch length!"
 110                 STDERR.puts "The unit of branch lengths must be 'substitution/site'"
 111                 STDERR.puts "If the unit is 'substition' in your tree, please"
 112                 STDERR.puts "use the scale argument,"
 113                 STDERR.puts "% newick2mafft scale in > out"
 114                 STDERR.puts "where scale = 1/(alignment length)"
 115                 STDERR.puts ""
 116                 exit 1
 117         end
 118
 119 #       STDERR.puts "subtree = " + $&
 120
 121         if memi[1] < memi[0] then
 122                 memi.reverse!
 123                 leni.reverse!
 124         end
 125
 126         tree.sub!( /XXX/, memi[0].to_s )
 127
 128         STDERR.puts "Tree = " + tree
 129
 130         printf( "%5d %5d %10.5f %10.5f\n", memi[0], memi[1], leni[0], leni[1] )
 131
 132 end