gegene 1.0.0 → 1.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/LICENSE.txt +21 -0
- data/lib/chromosome.rb +44 -0
- data/lib/genome.rb +11 -0
- data/lib/karyotype.rb +42 -4
- data/lib/population.rb +74 -21
- metadata +5 -4
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0599f2cbca99f724dacc4eb7f106122174108ea8
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data.tar.gz: c32d27d42638c9e12e292f615002663b8eae4581
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SHA512:
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metadata.gz:
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metadata.gz: 0144049db0f4c7634d21815c3b1c0d3e8b5347fb2167d82219b25e52112d1594f21710948e63e58c4196420ea63148d5fa0fab7ec14ade177982316f0e1c6583
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data.tar.gz: 3f54ddadf7ced812bd993cdc939a73ddebc26063302a502f753cef97e4d2d03c212616c241e9ecd1f97d130b9a8119661317b5491deed85006da3ef12a408049
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data/LICENSE.txt
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The MIT License (MIT)
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Copyright (c) 2013 Alexandre Ignjatovic
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/lib/chromosome.rb
CHANGED
@@ -1,26 +1,70 @@
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require 'gene'
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require 'allele'
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# This class represent a chromosome, which contains several allele (gene's values)
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# and is able to mutate, and to cross over.
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class Chromosome
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# Construct a chromosome from an array of alleles
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def initialize(alleles)
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raise "this constructor expect an array of alleles as input" unless
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alleles.is_a?(Array)
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@alleles = alleles
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end
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# Copy the current chromosome and all its alleles
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def copy
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Chromosome.new(@alleles.map{|allele| allele.copy })
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end
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# Create a random chromosome from a description
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def Chromosome.create_random_from(description)
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Chromosome.new(description.map{|gene| gene.create_random() })
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end
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# Returns the allele at a specific position
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def [](gene_position)
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@alleles[gene_position]
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end
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# Number of underlying alleles
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def size
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@alleles.size
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end
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# Mutate a randomly selected allele of the current chromosome
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def mutate
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allele_index = rand @alleles.size
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@alleles[allele_index].mutate()
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end
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# Aggregate all alleles values
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def aggregated_alleles()
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@alleles.map {|a| a.value}.join(";")
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end
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# Cross over two chromosomes to provide a new one
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def Chromosome.cross_over(chromosome_a, chromosome_b)
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if rand(2) == 0 then
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chromosome_a, chromosome_b =
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[chromosome_b, chromosome_a]
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end
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size = chromosome_a.size
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if size < 2 then
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return chromosome_a.copy
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elsif size == 2 then
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return Chromosome.new([chromosome_a[0],chromosome_b[1]])
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else
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swap_index = rand(size-1)
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index = 0
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new_alleles = []
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while (index < size) do
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new_alleles.push(
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(index <= swap_index ? chromosome_a : chromosome_b)[index].copy)
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index += 1
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end
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return Chromosome.new(new_alleles)
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end
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end
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end
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data/lib/genome.rb
CHANGED
@@ -1,7 +1,11 @@
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require 'Karyotype'
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# This class stands for the genome. It is a description of all
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# the gene describing a specific population.
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class Genome
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DEFAULT_CROSS_OVER_RATE = 0.01
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def initialize(genome_description)
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raise "Genome description MUST be an Array" unless genome_description.is_a? Array
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@chromosomes_description = []
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end
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@chromosomes_description << gene_array
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end
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@cross_over_rate = DEFAULT_CROSS_OVER_RATE
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end
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attr_accessor :gene_positions
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attr_reader :cross_over_rate
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def cross_over_rate=(rate)
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raise "cross_over_rate must be included in [0,1]" unless rate.between?(0,1)
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@cross_over_rate = rate
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end
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def get_gene_position(gene_name)
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@gene_positions[gene_name]
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end
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data/lib/karyotype.rb
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@@ -1,20 +1,30 @@
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require 'chromosome'
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require 'digest/md5'
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# This class represent a karyotype, which could be seen as a set of
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# chromosomes representing a specific individual of a population
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class Karyotype
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attr_accessor :chromosomes
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attr_accessor :fitness
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def initialize(genome, chromosomes_description)
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@genome = genome
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@chromosomes_description = chromosomes_description
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end
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private :initialize
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# Copy self and all its chromosomes to a new karyotype
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def copy
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karyotype = Karyotype.new(@genome, @chromosomes_description)
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karyotype.chromosomes = self.chromosomes.map{|chromosome| chromosome.copy}
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karyotype
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end
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def to_s
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@genome.gene_positions.keys.map{|gn| "#{gn}=>#{self[gn]}"}.join';'
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end
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# Create a random karyotype from a specific genome an its associated
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# chromosomes description
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def Karyotype.create_random_from(genome, chromosomes_description)
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karyotype = Karyotype.new(genome, chromosomes_description)
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karyotype.chromosomes = chromosomes_description.map {|description|
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karyotype
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end
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# Return the allele value of a specific named gene
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# We strongly recommand using symbols as gene name
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def [](gene_name)
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return nil if @chromosomes.nil?
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chromosome_position, gene_position =
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chromosome_position, gene_position =
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@genome.get_gene_position(gene_name)
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return nil if chromosome_position.nil? || gene_position.nil?
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return @chromosomes[chromosome_position][gene_position].value
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end
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# Breeding function
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# Create a new karyotype based on self and an other
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def +(other)
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child =
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child = Karyotype.new(@genome, @chromosomes_description)
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child.chromosomes = []
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other.chromosomes.each_with_index { |chromosome, index|
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child_chromosome = nil
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# Randomly copy chromosomes from dad or mom to child
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if (rand(100) / 100.0) < @genome.cross_over_rate then
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# Crossing over required
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child_chromosome =
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Chromosome.cross_over(chromosome, chromosomes[index])
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else
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# Standard breeding via random selection
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child_chromosome = (rand(2)==0?chromosome : chromosomes[index]).copy
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end
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child.chromosomes.push(child_chromosome)
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}
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child
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end
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# Aggregate all the allele into a md5 hash value
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def to_md5()
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if (@hash_value.nil?) then
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@hash_value = @chromosomes.map{ |chromosome|
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chromosome.aggregated_alleles
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}.join(";")
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@hash_value = Digest::MD5.hexdigest(@hash_value)
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end
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@hash_value
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end
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# Randomly mutate an allele of a randomly selected chromosome
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def mutate
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@chromosomes[rand @chromosomes.size].mutate
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self
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data/lib/population.rb
CHANGED
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DEFAULT_MUTATION_RATE = 0.01
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DEFAULT_KEEP_ALIVE_RATE = 0.1
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DEFAULT_EVOLVE_ITERATIONS = 1
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DEFAULT_FORCE_FITNESS_RECALCULATION = false
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attr_accessor :fitness_target, :karyotypes, :force_fitness_recalculation
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attr_reader :mutation_rate, :keep_alive_rate
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# mutation rate setter function
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# Accept values in the range [0,1]
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def mutation_rate=(value)
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raise "mutation_rate value must be included in [0,1]" unless value.between?(0,1)
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@mutation_rate = value
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end
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# keep alive rate setter function
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# Accept values in the range [0,1]
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def keep_alive_rate=(value)
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raise "mutation_rate value must be included in [0,1]" unless value.between?(0,1)
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@keep_alive_rate = value
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end
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# Run the fitness function for all karyotypes, and sort it by fitness
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def evaluate
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-
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if @force_fitness_recalculation then
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@karyotypes.each do |karyotype|
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karyotype.fitness = @fitness_calculator.call(karyotype)
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@fitness_hash[karyotype.to_md5()] = karyotype.fitness
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end
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else
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@karyotypes.each do |karyotype|
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if karyotype.fitness.nil? then
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if @fitness_hash[karyotype.to_md5()].nil? then
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karyotype.fitness = @fitness_calculator.call(karyotype)
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@fitness_hash[karyotype.to_md5()] = karyotype.fitness
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else
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karyotype.fitness = @fitness_hash[karyotype.to_md5()]
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end
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end
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end
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end
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@karyotypes.sort! { |x,y| y.fitness <=> x.fitness }
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end
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private :evaluate
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def initialize(size, genome, fitness_calculator)
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raise "size must be strictly positive." if size < 1
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@fitness_hash = {}
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@force_fitness_recalculation = DEFAULT_FORCE_FITNESS_RECALCULATION
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@mutation_rate = DEFAULT_MUTATION_RATE
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@keep_alive_rate = DEFAULT_KEEP_ALIVE_RATE
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@genome = Genome.new(genome)
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@karyotypes = Array.new(size){ @genome.create_random_karyotype }
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evaluate
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end
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-
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+
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def set_mutation_rate(rate)
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-
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raise "mutation_rate value must be included in [0,1]" unless rate.between?(0,1)
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@mutation_rate= rate
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self
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end
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-
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def set_keep_alive_rate(rate)
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raise "keep_alive_rate must be included in [0,1]" unless rate.between?(0,1)
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@keep_alive_rate = rate
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self
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end
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-
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+
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def set_fitness_target(target)
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@fitness_target = target
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self
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end
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-
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+
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def set_force_fitness_recalculation(target)
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@force_fitness_recalculation = target
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self
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end
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def size
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@karyotypes.size
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end
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def linear_random_select
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@karyotypes[rand @karyotypes.size]
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end
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-
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+
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def create_random_mutation
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linear_random_select.copy.mutate
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end
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private :linear_random_select, :create_random_mutation
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-
def
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def fitness_weighted_random_select
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@karyotypes[
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-
@karyotypes.size -
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@karyotypes.size -
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Integer(Math.sqrt(Math.sqrt(1 + rand(@karyotypes.size**4 - 1))))
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]
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end
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def random_breed
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-
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fitness_weighted_random_select + fitness_weighted_random_select
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end
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-
private :
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-
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private :fitness_weighted_random_select, :random_breed
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+
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# This function make ou population evolving by:
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# * Selecting and breeding the fittest karyotypes
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# * Running the fitness evaluation on all the newly created karyotyopes
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# The selection process include three subprocesses:
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# * Selecting the fittest individuals to keep alive
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# * Mutating randomly (linear) selected individuals
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# * Breeding randomly (fitness weighted) selected individuals
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def evolve(iterations = DEFAULT_EVOLVE_ITERATIONS)
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i = 1
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while (i <= iterations) &&
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(@fitness_target.nil? || @fitness_target > @karyotypes[0].fitness) do
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-
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-
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evolve_impl
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i += 1
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end
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self
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end
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-
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+
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def evolve_impl
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new_population = []
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-
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+
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# Keeping alive a specific amount of the best karyotypes
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keep_alive_count = Integer(@karyotypes.size * @keep_alive_rate)
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if keep_alive_count > 0 then
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@karyotypes[0, keep_alive_count].each {|karyotype| new_population.push(karyotype)}
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end
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-
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+
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139
|
mutation_count = Integer(@karyotypes.size * @mutation_rate)
|
87
140
|
(0..mutation_count-1).each {
|
88
141
|
new_population.push create_random_mutation
|
89
142
|
}
|
90
|
-
|
143
|
+
|
91
144
|
remaining = @karyotypes.size-mutation_count-keep_alive_count
|
92
145
|
(0..remaining-1).each {
|
93
146
|
child = random_breed
|
metadata
CHANGED
@@ -1,16 +1,16 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gegene
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.
|
4
|
+
version: 1.1.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Alexandre Ignjatovic
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2013-
|
11
|
+
date: 2013-11-01 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
|
-
description: Framework for
|
13
|
+
description: Framework for genetic algorithm fast development
|
14
14
|
email: alexandre.ignjatovic@gmail.com
|
15
15
|
executables: []
|
16
16
|
extensions: []
|
@@ -26,6 +26,7 @@ files:
|
|
26
26
|
- example/adding_gene_type.rb
|
27
27
|
- example/one_max.rb
|
28
28
|
- example/simple.rb
|
29
|
+
- LICENSE.txt
|
29
30
|
homepage: https://github.com/bankair/gegene
|
30
31
|
licenses:
|
31
32
|
- MIT
|
@@ -46,7 +47,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
46
47
|
version: '0'
|
47
48
|
requirements: []
|
48
49
|
rubyforge_project:
|
49
|
-
rubygems_version: 2.1.
|
50
|
+
rubygems_version: 2.1.10
|
50
51
|
signing_key:
|
51
52
|
specification_version: 4
|
52
53
|
summary: Genetic algorithm helpers
|