#!/usr/bin/env ruby

require 'rubygems'
require'bio'
include Bio
require 'apis'

dir = "/home/jbadger/Web/genomes/Archaeoglobus_fulgidus"

Dir.glob(dir + "/alignments/*").each {|file|
  count = 0
  File.new(file).each {|line|
    count += 1 if (line =~ /^\>/)
  }
  if (count < 16 && count > 9)
    name =  File.basename(file,".pir")
    ali = dir + "/alias/" + name  + ".ali"
    makeWeighborTree(name + "_weighbor.tree", file, name, ali)
    makeRindTree(name + "_rind.tree", file, name, ali)
    makeNJTree(name + "_NJ.tree", file, name, ali)
    makePuzzleTree(name + "_puz.tree", file, name, ali)
    makeProMLTree(name + "_ML.tree", file, name, ali)
    makeParsTree(name + "_pars.tree", file, name, ali) 
  end
}