Question

我有一个简单的类来模拟DNA字符串中的随机突变。它将随机（A C G T）字符引入随机位置。我想介绍一种指定变异率的方法。

有没有办法可以指定如何：

在给定错误率的情况下改变序列。（例如，千分之一）？
偏向突变的方法（更频繁地选择G - A或C - T）？

这是我当前的实现，仅处理随机更改。

class DNA
  attr_accessor :number_of_mutations
  attr_accessor :seq

  NUCLEOTIDES = ['A','C','T','G']

  #random positions
  def random_pos
    (1..seq.length).to_a.sample(number_of_mutations)
  end

  #pick a random nucleotide
  def random_nucleotide
    NUCLEOTIDES.sample
  end

  #generate a random seq
  def random_seq
    (1..number_of_mutations).map{NUCLEOTIDES[rand(NUCLEOTIDES.length)]}
  end

  def mutate
    #pick a random position
    positions = random_pos

    #pick a random nucleotide
    nucleotides = random_seq

    #insert the random nucleotide at the random position in the seq
    positions.zip(nucleotides).map do |pos,nuc|
      seq[pos] = nuc.downcase
    end
    seq
  end
end

d = DNA.new
d.number_of_mutations = 1
d.seq = "AAAAAA"
puts d.mutate  #will introduce a single random DNA base at a random location

Answer 1

首先，您应该实现一个以指定的速率返回正结果的函数。它可能是这样的：

# ==Function will return true with rate probability
def positive?(rate = 0.001) 
  rand((1/rate).round) == 0
end

或更复杂。

你可以用指定的速率实现突变机制。它可以是Mutators类的实例

class Mutator
  attr_reader :mutate_way, :probability

  def initialize(options = {})
    @mutate_way = options[:mutate_way]
    @probability = options[:probability]
  end

  def try_mutate        
    do_mutation if positive? @probability
  end  

  def do_mutation
    # your implementation based on @mutate_way
    # link it with DNA
  end
end

您可以定义许多突变，例如

mutations = [
  Mutator.new(:mutate_way => ['A', 'G'], :probability => 100),
  Mutator.new(:mutate_way => ['C', 'T'], :probability => 100),
  Mutator.new(:mutate_way => ['A', 'T'], :probability => 1000),
  Mutator.new(:mutate_way => ['C', 'G'], :probability => 1000)
]

并开始突变

d.number_of_mutations.times do
  mutations.each.map(&:try_mutate)
end

PS。代码示例可能有一些错误，这只是示例。

用红宝石突变DNA序列

1 个答案: