text: #!/usr/bin/env python
  __author__ = 'Sergei F. Kliver'
  
  import argparse, os
  
  from Bio import SeqIO
  from Bio.SeqUtils import GC
  
  import matplotlib
  matplotlib.use('Agg')
  import matplotlib.pyplot as plt
  plt.ioff()
  
  parser = argparse.ArgumentParser()
  
  parser.add_argument("-i", "--input_file", action="store", dest="input_file",
                      help="Input file with sequences")
  parser.add_argument("-o", "--output_prefix", action="store", dest="output_prefix",
                      help="Prefix of output files")
  parser.add_argument("-f", "--format", action="store", dest="format", default="fasta",
                      help="Format of input file. Default: fasta")
  parser.add_argument("-d", "--draw_histogram", action="store_true", dest="draw_hist", default=False,
                      help="Draw histogram of GC-content. Default: False")
  parser.add_argument("-s", "--use_species_names", action="store_true", dest="use_species_names",
                      help="Use species names instead of sequence ids")
  args = parser.parse_args()
  
  sequence_dict = SeqIO.index_db("temp.idx", args.input_file, args.format)
  
  GC_content_dict = {}
  
  
  with open("%s.stat" % args.output_prefix, "w") as stat_fd:
      #stat_fd.write("#scaffold\tGC-content\n")
      for record_id in sequence_dict:
          GC_content_dict[record_id] = GC(sequence_dict[record_id].seq)
          stat_fd.write("%s\t%.2f\n" % (sequence_dict[record_id].annotations["organism"] if args.use_species_names
                                                                                         else record_id,
                                        GC_content_dict[record_id]))
  
  if args.draw_hist:
      plt.figure(1, figsize=(6, 6))
      plt.subplot(1, 1, 1)
      plt.hist(GC_content_dict.values())
      plt.xlabel("GC content")
      plt.ylabel("N")
      plt.title("GC content")
  
      for ext in ".png", ".svg", ".eps":
          plt.savefig(args.output_prefix + ext)
  
  os.remove("temp.idx")