Source Code for Module Bio.HMM.Utilities

 1  """Generic functions which are useful for working with HMMs. 
 2   
 3  This just collects general functions which you might like to use in 
 4  dealing with HMMs. 
 5  """ 
 6   
 7   
 8 -def pretty_print_prediction(emissions, real_state, predicted_state, 
 9                              emission_title = "Emissions", 
10                              real_title = "Real State", 
11                              predicted_title = "Predicted State", 
12                              line_width = 75): 
13      """Print out a state sequence prediction in a nice manner. 
14   
15      Arguments: 
16   
17      o emissions -- The sequence of emissions of the sequence you are 
18      dealing with. 
19   
20      o real_state -- The actual state path that generated the emissions. 
21   
22      o predicted_state -- A state path predicted by some kind of HMM model. 
23      """ 
24      # calculate the length of the titles and sequences 
25      title_length = max(len(emission_title), len(real_title), 
26                         len(predicted_title)) + 1 
27      seq_length = line_width - title_length 
28   
29      # set up the titles so they'll print right 
30      emission_title = emission_title.ljust(title_length) 
31      real_title = real_title.ljust(title_length) 
32      predicted_title = predicted_title.ljust(title_length) 
33   
34      cur_position = 0 
35      # while we still have more than seq_length characters to print 
36      while 1: 
37          if (cur_position + seq_length) < len(emissions): 
38              extension = seq_length 
39          else: 
40              extension = len(emissions) - cur_position 
41   
42          print "%s%s" % (emission_title, 
43                          emissions[cur_position:cur_position + seq_length]) 
44          print "%s%s" % (real_title, 
45                          real_state[cur_position:cur_position + seq_length]) 
46          print "%s%s\n" % (predicted_title, 
47                            predicted_state[cur_position: 
48                                            cur_position + seq_length]) 
49   
50          if (len(emissions) < (cur_position + seq_length)): 
51              break 
52   
53          cur_position += seq_length 
54