tmapっぽい形式のファイルから全遺伝子IDそれぞれのwigファイル(bedgraph format)を作成します．

bedgraph.rb

#/usr/bin/env ruby
require "pp"
require "optparse"

# Usage : ruby bedgraph.rb [-o output_dir] input_file
# Output_dir is optional. Default output_dir is "bedgraph".
#
# Input_file format must be tab delimited file and the following format below.
# gene_id  gene_name  fpkm  chr  start  end
#
# Please change the number a[n] (line 22) if your input_file formtat is different form it.

def open_t_delimited_file(filename)
  h = Hash.new([])
  id = []

  open(filename) {|f|
    f.each_line do |line|
      a = line.chomp.split("\t")
      if a[0][0] != ?-
        id << a[0]
        id_sym = a[0].to_sym
        h[id_sym] += [["chr" + a[3], a[4], a[5], a[2]]] # chr,start,end,fpkm
      end
    end
  }

  puts filename + " was loaded."
  return h, id
end

if __FILE__ == $PROGRAM_NAME
  output_dir = "bedgraph"
  ARGV.options do |opt|
    opt.on( '-o VAL' ) { |a| output_dir = a }
    opt.parse!
  end

  tmap, gene_id_list = open_t_delimited_file(ARGV[0])

  gene_id_list_sorted = gene_id_list.uniq

  if output_dir[-1] == ?/
    output_dir = output_dir[0..-2]
  end
  if File.exists?(output_dir)
    puts %|ERROR : "#{output_dir}" directory already exists!|
    exit 1
  end
  Dir.mkdir(output_dir)

  gene_id_list_sorted.each do |i|
    output_list = tmap[i.to_sym].sort{|a,b| a[1] <=> b[1]}.map{|e| e.join("\t")}

    open("#{output_dir}/#{i}.txt","w") {|f|
      f.puts "track type=bedGraph name=\"fpkm #{i}\" visibility=full"
      f.puts output_list
    }
  end

  current_dir = Dir.pwd
  puts "output : #{current_dir}/#{output_dir}"
end