getAAfromdNdS

#!/usr/bin/env ruby

require 'ostruct'
require 'optparse'
require 'rubygems'
require'bio'
include Bio
opt.threshold = 0.8
opt = OpenStruct.new

ARGV.options {|opts|
  opts.banner << " dnsds.txt alignment"
  opts.on("-t ", "--threshold", Float,
	  "threshold to report (#{opt.threshold})") {|t| opt.threshold = t}
  begin
    opts.parse!
  rescue
    STDERR.puts $!.message
    STDERR.puts opts
    exit(1)
  end
  if (ARGV.size != 2)
    STDERR.puts opts
    exit(1)
  end
}

dnds, afa = ARGV

seqs = []
FlatFile.new(FastaFormat, File.new(afa)).each {|seq|
  seqs.push(seq.seq)
}

File.new(dnds).each {|line|
  num, w = line.split(" ")
  num = num.to_i
  w = w.to_f.abs
  aas = Hash.new
  if (w >= opt.threshold)
    seqs.each {|seq|
      aas[seq[num - 1].chr] = true 
    }
    printf("%d\t%.2f\t%s\n",num, w, aas.keys.sort.to_s)
  end
}