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Sourcecode: python-biopython version File versions


00001 """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
# standard library
import random

00011 class AmbiguousRepair:
    """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.
00020     def __init__(self, ambig_finder, num_ambiguous):
        """Initialize the repair class.


        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()

00038     def repair(self, organism):
        """Perform a repair to remove excess ambiguous genes.
        new_org = organism.copy()
        # start getting rid of ambiguous items
        while 1:
            # first find all of the ambigous items
            seq_genome = new_org.genome.toseq()
            all_ambiguous = self._ambig_finder.find_ambiguous(seq_genome.data)

            # if we have less then the number of ambiguous allowed, stop
            if len(all_ambiguous) <= self._num_ambiguous:

            # 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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