Source Code for Module Bio.GA.Repair.Stabilizing

 1  """Methods for performing repairs that will Stabilize genomes. 
 2   
 3  These methods perform repair to keep chromosomes from drifting too far in 
 4  any direction -- ie. bring them back to a stabilizing center. This may be 
 5  useful in cases where fitness functions alone won't keep chromosomes in 
 6  check. 
 7  """ 
 8  # standard library 
 9  import random 
10   
11   
12 -class AmbiguousRepair(object): 
13      """Perform repair to reduce the number of Ambiguous genes in a genome. 
14   
15      In cases where ambiguous genes are allowed in a genome (for example, 
16      where you have a wild card character like '*' that will match 
17      anything), these can come to dominate a genome since, really, the 
18      best fitness is someting like '*******'. This repair protects against 
19      that by changing ambiguous characters into some non-ambiguous gene. 
20      """ 
21 -    def __init__(self, ambig_finder, num_ambiguous): 
22          """Initialize the repair class. 
23   
24          Arguments: 
25   
26          o ambig_finder - A class implementing the function find_ambiguous 
27          which will return a list of all ambiguous positions in a sequence. 
28          It also must have the function all_unambiguous, which will return 
29          all allowed unambiguous letters. 
30   
31          o num_ambiguous - The minimum number of ambiguous items that are 
32          allowed in a genome. If there are more than this present, repair 
33          will be performed. 
34          """ 
35          self._ambig_finder = ambig_finder 
36          self._num_ambiguous = num_ambiguous 
37          self._alphabet_letters = ambig_finder.all_unambiguous() 
38   
39 -    def repair(self, organism): 
40          """Perform a repair to remove excess ambiguous genes. 
41          """ 
42          new_org = organism.copy() 
43   
44          # start getting rid of ambiguous items 
45          while 1: 
46              # first find all of the ambigous items 
47              seq_genome = new_org.genome.toseq() 
48              all_ambiguous = self._ambig_finder.find_ambiguous(str(seq_genome)) 
49   
50              # if we have less then the number of ambiguous allowed, stop 
51              if len(all_ambiguous) <= self._num_ambiguous: 
52                  break 
53   
54              # remove an ambiguous item and replace it with a non-ambiguous 
55              to_change = random.choice(all_ambiguous) 
56              new_gene = random.choice(self._alphabet_letters) 
57              new_org.genome[to_change] = new_gene 
58   
59          return new_org 
60