def swap_mutation(contig_ord, memo, subset_memo, mut_rate=MUTATION):
# for swap mutation protocol see http://www.theprojectspot.com/tutorial-post/applying-a-genetic-algorithm-to-the-travelling-salesman-problem/5
a = sampler(mut_rate, 1)[0]
new = [i for i in contig_ord.chrom_list]
pos = range(len(new))
random.shuffle(pos)
for i in range(a):
sign = random.choice([-1, 1])
p1 = pos.pop(0)
p2 = pos.pop(0)
tmp = new[p1]
new[p1] = new[p2] * sign
new[p2] = tmp * sign
c = ContigOrder(new, chrom_dict, scaff_lookup, memo, subset_memo)
return c
def swap_mutation(contig_ord, mut_rate = MUTATION):
#for swap mutation protocol see http://www.theprojectspot.com/tutorial-post/applying-a-genetic-algorithm-to-the-travelling-salesman-problem/5
a = sampler(mut_rate, 1)[0]
new = [i for i in contig_ord.chrom_list]
pos = range(len(new))
random.shuffle(pos)
for i in range(a):
sign = random.choice([-1, 1])
p1 = pos.pop(0)
p2 = pos.pop(0)
tmp = new[p1]
new[p1] = new[p2]*sign
new[p2] = tmp*sign
c = ContigOrder(new, chrom_dict, scaff_lookup)
return c
def recombination(contig_ord1, contig_ord2):
#use order crossover (see: http://www.theprojectspot.com/tutorial-post/applying-a-genetic-algorithm-to-the-travelling-salesman-problem/5)
parents = [[i for i in contig_ord1.chrom_list], [i for i in contig_ord2.chrom_list]]
random.shuffle(parents)
contig_ord1, contig_ord2 = parents #just scramble which parent is donor, so p2 isn't always
new = ['-' for i in contig_ord1]
pos = range(len(new))
a,b = sorted(sampler(pos, 2))
sval = set([abs(i) for i in contig_ord2[a:b+1]])
sidx = set(range(a,b+1))
for i in range(a, b+1): new[i] = contig_ord2[i]
picks = [i for i in contig_ord1 if abs(i) not in sval]
for i in [j for j in range(len(contig_ord1)) if j not in sidx]:
p = picks.pop(0)
new[i] = p
c = ContigOrder(new, chrom_dict, scaff_lookup)
return c
def recombination(contig_ord1, contig_ord2, memo, subset_memo):
#use order crossover (see: http://www.theprojectspot.com/tutorial-post/applying-a-genetic-algorithm-to-the-travelling-salesman-problem/5)
parents = [[i for i in contig_ord1.chrom_list], [i for i in contig_ord2.chrom_list]]
random.shuffle(parents)
contig_ord1, contig_ord2 = parents #just scramble which parent is donor, so p2 isn't always
new = ['-' for i in contig_ord1]
pos = range(len(new))
a,b = sorted(sampler(pos, 2))
sval = set([abs(i) for i in contig_ord2[a:b+1]])
sidx = set(range(a,b+1))
for i in range(a, b+1): new[i] = contig_ord2[i]
picks = [i for i in contig_ord1 if abs(i) not in sval]
for i in [j for j in range(len(contig_ord1)) if j not in sidx]:
p = picks.pop(0)
new[i] = p
c = ContigOrder(new, chrom_dict, scaff_lookup, memo, subset_memo)
return c
