#!/usr/bin/env ruby

require 'rubygems'
require 'optimist'
require 'bio'    

# converts pointless stockholm alignment to a useful fasta one
def stockholm2Fasta(alignFile)
   afa = alignFile + ".afa"
   afaf = File.new(afa, "w")
   seqs = Hash.new
   start = false
   File.new(alignFile).each do |line|
      if (line =~ /^#|\/\//)
         start = true
         next
      end
      next if !start
      name, ali = line.split(" ")
      next if (!start || ali.nil?)
      ali.gsub!(".","-")
      seqs[name] = "" if (seqs[name].nil?)
      seqs[name] += ali += "\n"
   end
   seqs.keys.each do |name|
      afaf.printf(">%s\n%s",name,seqs[name])
   end
   afaf.close
   afa
end

# infers tree by desired method, populates db, returns tree
def infer(pid, afa, method, verbose)
   STDERR << "Making tree for " << pid << "...\n" if verbose
   ali = aliasFasta(afa, nil, afa + ".ali")
   tree = nil
   if (method == "nj")
      stock = fasta2Stockholm(afa + ".ali")
      nj = `quicktree -boot 100 '#{stock}'`
      tree = NewickTree.new(nj.tr("\n",""))
      tree.unAlias(ali)
      tree.midpointRoot
   end
   File.unlink(stock) if File.exists?(stock)
   File.unlink(afa + ".ali") if File.exists?(afa + ".ali")
   tree
end

ARGV.push("--help") if ARGV.empty?
opts = Optimist::options do
  banner File.basename($0)
  opt :input, "Input stockholm file", :required=>true, :type=>:string
end

stockholm2Fasta(opts.input)