source: branches/lib/GDE/MAFFT/mafft-7.055-with-extensions/core/newick2mafft.rb

#! /usr/bin/env ruby

#version 2, 2009/01/24


if ARGV.length == 1
        scale = 1.0
elsif ARGV.length == 2
        scale = ARGV.shift.to_f
else
        STDERR.puts "USAGE: newick2mafft.rb scale input_tree > output"
        exit
end

if scale <= 0.0 then
        STDERR.puts "Inappropriate scale, #{scale.to_s}"
        exit
end

STDERR.puts "scale = " + scale.to_s

infp = File.open( ARGV.shift, "r" )

tree = ""
while line = infp.gets
        tree += line.strip
        break if tree =~ /;$/
end
infp.close


#tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "").gsub(/:\-[0-9\.]+/, ":0.0" )
tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "")


STDERR.puts "Initial tree = " +  tree

def resolve( tree )


while 1
#       p tree
        tree.sub!( /\,([0-9]+):(\-?[0-9\.]+)\,([0-9]+):(\-?[0-9\.]+)/, ",XXX" )
        hit1 = $1
        hit2 = $2
        hit3 = $3
        hit4 = $4

#       p hit1
#       p hit2
#       p hit3
#       p hit4

#       puts "introduce XXX"
#       p tree

        break unless tree.index(/XXX/)

        poshit = tree.index(/XXX/)
#       puts "poshit=" + poshit.to_s

        i = poshit
        height = 0
        while i >= 0
                break if height == 0 && tree[i..i] == '('
                if tree[i..i] == ')' then
                        height += 1
                elsif tree[i..i] == '(' then
                        height -= 1
                end
                i -= 1
        end

        poskakko = i
#       puts "poskakko = " + poskakko.to_s
        zenhan = tree[0..poskakko]
        zenhan = "" if poskakko == -1
#       puts "zenhan = " + zenhan

        treelen = tree.length
        tree = zenhan + "(" + tree[poskakko+1..treelen]
#       puts "add ("
#       p tree
        tree.sub!( /XXX/, "#{hit1}:#{hit2}):0,#{hit3}:#{hit4}" )

#       p tree
end


return tree

end

memi = [-1,-1]
leni = [-1,-1]

while tree.index( /\(/ ) 

        tree = resolve( tree )

        tree.sub!( /\(([0-9]+):(\-?[0-9\.]+),([0-9]+):(\-?[0-9\.]+)\)/, "XXX" )
        memi[0] = $1.to_i
        leni[0] = $2.to_f * scale
        memi[1] = $3.to_i
        leni[1] = $4.to_f * scale

        if leni[0] > 10 || leni[1] > 10 then
                STDERR.puts ""
                STDERR.puts "Please check the scale of branch length!"
                STDERR.puts "The unit of branch lengths must be 'substitution/site'"
                STDERR.puts "If the unit is 'substition' in your tree, please"
                STDERR.puts "use the scale argument,"
                STDERR.puts "% newick2mafft scale in > out"
                STDERR.puts "where scale = 1/(alignment length)"
                STDERR.puts ""
                exit 1
        end

#       STDERR.puts "subtree = " + $&

        if memi[1] < memi[0] then
                memi.reverse!
                leni.reverse!
        end

        tree.sub!( /XXX/, memi[0].to_s )

#       STDERR.puts "Tree = " + tree

        printf( "%5d %5d %10.5f %10.5f\n", memi[0], memi[1], leni[0], leni[1] )

end