Source Code for Module object_to_circos

  1  #! /usr/local/bin/python 
  2  #-*- coding: utf-8 -*- 
  3   
  4  """object_to_circos 
  5   
  6  Loads a serialized graph object in memory and generates an input file 
  7  for Circos (matrix). 
  8  """ 
  9   
 10  __author__ = "Jerome Hussenet, Cedric Bonhomme" 
 11  __version__ = "$Revision: 0.4 $" 
 12  __date__ = "$Date: 2009/03/14 $" 
 13  __copyright__ = "Copyright (c) 2009 Jerome Hussenet, Copyright (c) 2009 Cedric Bonhomme" 
 14  __license__ = "Python" 
 15   
 16  import os 
 17  import sys 
 18   
 19  import pickle 
 20   
 21   
 22 -def object_to_circos(obj_file, circos_file): 
 23      """Create the input file for Circos. 
 24      """ 
 25      if options.verbose: 
 26          print "Loading objet..." 
 27      dic_obj = open(obj_file, "r") 
 28      dic_ip = pickle.load(dic_obj) 
 29   
 30      if options.verbose: 
 31          print "Searching IP that are source and destination..." 
 32      ip_state = {} 
 33      for ip_src in dic_ip: 
 34          if ip_src not in ip_state: 
 35              ip_state[ip_src] = 1 
 36          elif ip_state[ip_src] == 2: 
 37              ip_state[ip_src] += 1 
 38   
 39          for ip_dst in dic_ip[ip_src]: 
 40              if ip_dst not in ip_state: 
 41                  ip_state[ip_dst] = 2 
 42              elif ip_state[ip_dst] == 1: 
 43                  ip_state[ip_dst] += 2 
 44   
 45      liste_ip = [] 
 46      for ip in ip_state: 
 47          if ip_state[ip] == 3: 
 48              liste_ip.append(ip) 
 49   
 50      if options.verbose: 
 51          print "Circos matrix generation..." 
 52      # build the table s/d 
 53      # first dimension : source ip 
 54      # second dimension : destination ip 
 55      # data : relations number 
 56      tab = {} 
 57      for i in liste_ip: 
 58          tab[i] = {} 
 59          for j in dic_ip[i]: 
 60              if ip_state[j] == 3: 
 61                  tab[i][j] = dic_ip[i][j] 
 62          tab[i][i] = "-" 
 63   
 64      # Freeing memory 
 65      del dic_ip 
 66      del liste_ip 
 67      del ip_state 
 68   
 69      if options.verbose: 
 70          print "Saving the matrix..." 
 71      tab_file = open(circos_file, "wb") 
 72      s= [] 
 73      s.append("ip") 
 74      for i in tab: 
 75          s.append(i) 
 76      tab_file.write("\t".join(s) + "\n") 
 77   
 78      for i in tab: 
 79          s = [] 
 80          s.append(i) 
 81          for j in tab: 
 82              try: 
 83                  s.append(str(tab[i][j])) 
 84              except: 
 85                  s.append("0") 
 86          tab_file.write("\t".join(s) + "\n") 
 87   
 88      tab_file.close() 
 89   
 90   
 91  if __name__ == "__main__": 
 92      # Point of entry in execution mode. 
 93      from optparse import OptionParser 
 94      parser = OptionParser() 
 95      parser.add_option("-i", "--input", dest="obj_file", 
 96                      help="Python serialized object") 
 97      parser.add_option("-o", "--output", dest="circos_file", 
 98                      help="Circos file") 
 99      parser.add_option("-q", "--quiet", 
100                      action="store_false", dest="verbose", 
101                      help="be vewwy quiet (I'm hunting wabbits)") 
102      parser.set_defaults(obj_file = './data/dic.pyobj', 
103                      circos_file = './data/ip.circos', 
104                      verbose = True) 
105   
106      (options, args) = parser.parse_args() 
107   
108      object_to_circos(options.obj_file, options.circos_file) 
109