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|
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""
Generalized N-Point Crossover.
For even values of N, perform N point crossover
(select N/2 points each in the two genomes, and alternate)
For odd values of N, perform symmetric N+1 point crossover
(select N/2 points for both genomes)
N-Point introduction (my notation):
| genome 1: A-----B-----C-----D-----E-----F-----G
| genome 2: a=====b=====c=====d=====e=====f=====g
|
| 2-point, symmetric (points=1):
| A-----B-----C- 1 -D-----E-----F-----G
| a=====b=====c= 2 =d=====e=====f=====g
| returns: (ABCdefg, abcDEFG)
|
| 2-point, asymmetric (points=2):
| A-----B- 1 -C-----D-----E-----F-----G
| a=====b=====c=====d=====e= 2 =f=====g
| returns: (ABfg, abcdeCDEFG)
and for the drastic (n can be arbitrary to the length of the genome!):
| 12-point, symmetric (points=11):
| A- 1 -B- 2 -C- 3 -D- 4 -E- 5 -F- 6 -G
| a= 7 =b= 8 =c= 9 =d= 10 e= 11 f= 12 g
| returns: (AbCdEfG, aBcDeFg)
| (note that points=12 will yield the same result, but 11
| may be somewhat faster)
"""
# standard modules
import random
from Bio._py3k import range
class GeneralPointCrossover(object):
"""Perform n-point crossover between genomes at some defined rates.
Ideas on how to use this class:
- Call it directly ( construct, do_crossover )
- Use one of the provided subclasses
- Inherit from it:
* replace _generate_locs with a more domain
specific technique
* replace _crossover with a more efficient
technique for your point-count
"""
def __init__(self, points, crossover_prob=.1):
"""Initialize to do crossovers at the specified probability.
"""
self._crossover_prob = crossover_prob
self._sym = points % 2 # odd n, gets a symmetry flag
self._npoints = (points + self._sym) // 2 # (N or N+1)//2
def do_crossover(self, org_1, org_2):
"""Potentially do a crossover between the two organisms.
"""
new_org = (org_1.copy(), org_2.copy())
# determine if we have a crossover
crossover_chance = random.random()
if crossover_chance <= self._crossover_prob:
# pre-compute bounds (len(genome))
bound = (len(new_org[0].genome), len(new_org[1].genome))
mbound = min(bound)
# can't have more than 0,x_0...x_n,bound locations
if (self._npoints == 0 or self._npoints > mbound - 2):
self._npoints = mbound - 2
y_locs = []
# generate list for the shortest of the genomes
x_locs = self._generate_locs(mbound)
if (self._sym != 0):
y_locs = x_locs
else:
# figure out which list we've generated
# for, and generate the other
if (mbound == bound[0]):
y_locs = self._generate_locs(bound[1])
else:
y_locs = x_locs
xlocs = self._generate_locs(bound[0])
# copy new genome strings over
tmp = self._crossover(0, new_org, (x_locs, y_locs))
new_org[1].genome = self._crossover(1, new_org, (x_locs, y_locs))
new_org[0].genome = tmp
return new_org
def _generate_locs(self, bound):
"""Generalized Location Generator:
arguments:
- bound (int) - upper bound
returns: [0]+x_0...x_n+[bound]
where n=self._npoints-1
and 0 < x_0 < x_1 ... < bound
"""
results = []
for increment in range(self._npoints):
x = random.randint(1, bound - 1)
while (x in results): # uniqueness
x = random.randint(1, bound - 1)
results.append(x)
results.sort() # sorted
return [0] + results + [bound] # [0, +n points+, bound]
def _crossover(self, x, no, locs):
"""Generalized Crossover Function:
arguments:
- x (int) - genome number [0|1]
- no (organism,organism)
- new organisms
- locs (int list, int list)
- lists of locations,
[0, +n points+, bound]
for each genome (sync'd with x)
return type: sequence (to replace no[x])
"""
s = no[x].genome[:locs[x][1]]
for n in range(1, self._npoints):
# flipflop between genome_0 and genome_1
mode = (x + n) % 2
# _generate_locs gives us [0, +n points+, bound]
# so we can iterate: { 0:loc(1) ... loc(n):bound }
t = no[mode].genome[locs[mode][n]:locs[mode][n + 1]]
if (s):
s = s + t
else:
s = t
return s
class TwoCrossover(GeneralPointCrossover):
"""Helper class for Two Point crossovers.
Offers more efficient replacements to the GeneralPoint framework
for single pivot crossovers
"""
def _generate_locs(self, bound):
"""Replacement generation.
See GeneralPoint._generate_locs documentation for details
"""
return [0, random.randint(1, bound - 1), bound]
def _crossover(self, x, no, locs):
"""Replacement crossover
see GeneralPoint._crossover documentation for details
"""
y = (x + 1) % 2
return no[x].genome[:locs[x][1]] + no[y].genome[locs[y][1]:]
class InterleaveCrossover(GeneralPointCrossover):
"""Demonstration class for Interleaving crossover.
Interleaving: AbCdEfG, aBcDeFg
"""
def __init__(self, crossover_prob=0.1):
GeneralPointCrossover.__init__(self, 0, crossover_prob)
def _generate_locs(self, bound):
return list(range(-1, bound + 1))
def _crossover(self, x, no, locs):
s = no[x].genome[0:1]
for n in range(1, self._npoints + 2):
mode = (x + n) % 2
s += no[mode].genome[n:n + 1]
return s + no[mode].genome[self._npoints + 3:]
|
