Source Code for Module Bio.GA.Mutation.Simple

 1  """Perform Simple mutations on an organism's genome. 
 2  """ 
 3  # standard modules 
 4  import random 
 5   
 6   
 7 -class SinglePositionMutation(object): 
 8      """Perform a conversion mutation, but only at a single point in the genome. 
 9   
10      This does not randomize the genome as much as ConversionMutation, since 
11      only one change is allowed per genome at the specified mutation rate. 
12      """ 
13 -    def __init__(self, mutation_rate = 0.001): 
14          """Initialize a mutator. 
15   
16          Arguments: 
17   
18          o mutation_rate - The chance of a mutation happening once in the 
19          genome. 
20          """ 
21          self._mutation_rate = mutation_rate 
22          # a random number generator to test if we have a mutation 
23          self._mutation_rand = random.Random() 
24          # a random number generator to switch to a new alphabet letter 
25          self._switch_rand = random.Random() 
26          # a random number generator to find the mutation position 
27          self._pos_rand = random.Random() 
28   
29 -    def mutate(self, organism): 
30          """Mutate the organisms genome. 
31          """ 
32          mutated_org = organism.copy() 
33          gene_choices = mutated_org.genome.alphabet.letters 
34   
35          mutation_chance = self._mutation_rand.random() 
36          if mutation_chance <= self._mutation_rate: 
37              # pick a gene position to mutate at 
38              mutation_pos = \ 
39                           self._pos_rand.choice(range(len(mutated_org.genome))) 
40   
41              # get a new letter to replace the position at 
42              new_letter = self._switch_rand.choice(gene_choices) 
43   
44              mutated_org.genome[mutation_pos] = new_letter 
45   
46          return mutated_org 
47   
48   
49 -class ConversionMutation(object): 
50      """Potentially mutate any item to another in the alphabet. 
51   
52      This just performs switching mutation -- changing one gene of a genome 
53      to any other potential gene, at some defined frequency. If the organism 
54      is determined to mutate, then the alphabet item it is equally likely 
55      to switch to any other letter in the alphabet. 
56      """ 
57 -    def __init__(self, mutation_rate = 0.001): 
58          """Inititialize a mutator. 
59   
60          Arguments: 
61   
62          o mutation_rate -- The chance of a mutation happening at any 
63          position in the genome. 
64          """ 
65          self._mutation_rate = mutation_rate 
66          # a random number generator to test if we have a mutation 
67          self._mutation_rand = random.Random() 
68          # a random number generator to switch to a new alphabet letter 
69          self._switch_rand = random.Random() 
70   
71 -    def mutate(self, organism): 
72          """Mutate the organisms genome. 
73          """ 
74          mutated_org = organism.copy() 
75   
76          gene_choices = mutated_org.genome.alphabet.letters 
77   
78          # potentially mutate any gene in the genome 
79          for gene_index in range(len(mutated_org.genome)): 
80              mutation_chance = self._mutation_rand.random() 
81              # if we have a mutation 
82              if mutation_chance <= self._mutation_rate: 
83                  # get a new letter 
84                  new_letter = self._switch_rand.choice(gene_choices) 
85                  mutated_org.genome[gene_index] = new_letter 
86   
87          return mutated_org 
88