Compare metal distances across internal nodes of a tree

metaltree.rb

#!/usr/bin/env ruby                                                                                                                                   
                                                                                                                                                      
require 'bio'                                                                                                                                         
require 'tempfile'
                                                                                                                                                      
@tmp=Dir.mktmpdir

                                                                                                                                                      
@tree=Bio::Newick.new(File.read(ARGV.shift)).tree                                                                                                                      
@s1={}
@s2={}

Bio::FlatFile.auto(ARGV.shift).each_entry do  |e|
        @s1[e.entry_id.gsub('_',' ')]=e
end
Bio::FlatFile.auto(ARGV.shift).each_entry do  |e|
        @s2[e.entry_id.gsub('_',' ')]=e
end

def calc_score(node)
        return 0 if (@tree.children(node).length==0)
        seqs = @tree.leaves(node).map{|x| x.name}

        File.open(@tmp + "/f1","w") do |f|
              seqs.each do |s|
                      f.puts @s1[s]
              end
        end
        File.open(@tmp + "/f2","w") do |f|
              seqs.each do |s|
                      f.puts @s2[s]
              end
        end
        print seqs.join(",") + " " 
        puts `metal #{ARGV.join(" ")} #{@tmp}/f1 #{@tmp}/f2`
end

@tree.nodes.map{|x| calc_score(x)}