Method: String#mutation

Defined in:
lib/viral_seq/string.rb

#mutation(error_rate = 0.01) ⇒ String

mutate a nt sequence (String class) randomly

Examples:

mutate a sequence at an error rate of 0.05

seq = "TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTG"
seq.mutation(0.05)
=> "TGGAAGGGCTAATGCACTCCCAACGAAGACACGATATCCTTGATCTGTGGATCTACGACACACAAGGCTGCTTCCCTG"



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# File 'lib/viral_seq/string.rb', line 23

def mutation(error_rate = 0.01)
  new_string = ""
  self.split("").each do |nt|
    pool = ["A","C","T","G"]
    pool.delete(nt)
    s = error_rate * 10000
    r = rand(10000)
    if r < s
      nt = pool.sample
    end
    new_string << nt
  end
  return new_string
end