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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.
#
"""Methods for performing repairs that will Stabilize genomes.
These methods perform repair to keep chromosomes from drifting too far in
any direction -- ie. bring them back to a stabilizing center. This may be
useful in cases where fitness functions alone won't keep chromosomes in
check.
"""
# standard library
import random
class AmbiguousRepair(object):
"""Perform repair to reduce the number of Ambiguous genes in a genome.
In cases where ambiguous genes are allowed in a genome (for example,
where you have a wild card character like '*' that will match
anything), these can come to dominate a genome since, really, the
best fitness is someting like '*******'. This repair protects against
that by changing ambiguous characters into some non-ambiguous gene.
"""
def __init__(self, ambig_finder, num_ambiguous):
"""Initialize the repair class.
Arguments:
o ambig_finder - A class implementing the function find_ambiguous
which will return a list of all ambiguous positions in a sequence.
It also must have the function all_unambiguous, which will return
all allowed unambiguous letters.
o num_ambiguous - The minimum number of ambiguous items that are
allowed in a genome. If there are more than this present, repair
will be performed.
"""
self._ambig_finder = ambig_finder
self._num_ambiguous = num_ambiguous
self._alphabet_letters = ambig_finder.all_unambiguous()
def repair(self, organism):
"""Perform a repair to remove excess ambiguous genes.
"""
new_org = organism.copy()
# start getting rid of ambiguous items
while True:
# first find all of the ambigous items
seq_genome = new_org.genome.toseq()
all_ambiguous = self._ambig_finder.find_ambiguous(str(seq_genome))
# if we have less then the number of ambiguous allowed, stop
if len(all_ambiguous) <= self._num_ambiguous:
break
# remove an ambiguous item and replace it with a non-ambiguous
to_change = random.choice(all_ambiguous)
new_gene = random.choice(self._alphabet_letters)
new_org.genome[to_change] = new_gene
return new_org
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