Psychic bug

[Gerard Flanagan]

Jennifer Hallinan wrote:
> Hi,
>
> I have a mutate function for a genetic algorithm which is giving me
> odd results. I suspect I'm missing somthing really simple, so I'd be
> grateful for any suggestions. Basically, when I comment out the line
> which is commented out below, it works fine (although of course it
> doesn't change the genome). When I uncomment it gen[letter]
> automagically gets the value base in the print statements, before the
> assignment has been made. And it still doesn't update the genome.
> Genome is a string of integers in the range 0- 3, hence the
> conversion.
>
>     def Mutate(self, mrate):
>         g = Random(rseed)
>         # If no mutation rate specified, use 1 per genome
>         if mrate == -1:
>             mrate = 1.0/len(self.genome)
>         print "mrate is ", mrate
>
>         print "original genome: "
>         print self.genome
>         # convert genome to a list
>         gen = [ord(letter)-48 for letter in self.genome]
>
>         for letter in range(len(gen)):
>             rnum = g.random()
>             if rnum < mrate:
>                 base = g.randint(0,3)
>                 print "base is ", base
>                 print "pos ", letter, gen[letter], " to ", base
> #                gen[letter] = base
>
>         # convert list back to a string
>         self.genome = ''.join([str(x) for x in gen])
>         print "final genome"
>         print self.genome
>
[...]
>
> Thanks,
>
> Jen


Jen

how about storing the genome data as a list, then converting to a
string if needs be?


import random

class Genome(object):

    def __init__(self, genome):
        self.genome = list(genome)
        self.mrate = 1.0/len(genome)

    def __str__(self):
        return ''.join(self.genome)

    def Mutate(self):
        for i in range(len(self.genome)):
            if random.random() < self.mrate:
                self.genome[i] = str(random.randint(0,2))


print
G = Genome( '10021010212021110' )
print G
G.Mutate()
print G
G.mrate = 0.8
G.Mutate()
print G


Gerard