Bioinformatics/Sequence mutation: Difference between revisions

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=={{header|Ruby}}==

<lang ruby>class DNA_Seq

attr_accessor :seq

def initialize(bases: %i[A C G T] , size: 0)

@bases = bases

@seq = Array.new(size){ bases.sample }

end

def mutate( n=10 )

n.times{|n| method([:s, :d, :i].sample).call}

end

def to_s(n = 50)

just_size = @seq.size / n

(0...@seq.size).step(n).map{|from| "#{from.to_s.rjust(just_size)} " + @seq[from, n].join}.join("\n") +

"\nTotal #{seq.size}: #{@seq.tally.sort.to_h.inspect}\n\n"

end

def s = @seq[rand_index]= @bases.sample

def d = @seq.delete_at(rand_index)

def i = @seq.insert(rand_index, @bases.sample )

alias :swap :s

alias :delete :d

alias :insert :i

private

def rand_index = rand( @seq.size )

end

puts test = DNA_Seq.new(size: 200)

test.mutate

puts test

test.delete

puts test

</lang>

{{out}}

<pre> 0 TAAGGTGAGGAGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA

50 CTCACCCATACTCGCCTCTGAAGCATGTTTTACTTGGATAGGGCCTACAG

100 CAGTATTCACCCATTCCTCGGCTCCTGACCTGATGTAGGTCTATGTGCGG

150 GAAAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAGGC

Total 200: {:A=>51, :C=>50, :G=>52, :T=>47}

0 TAAGCTGAGGTGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA

50 CTCACCCATACTCGCCTCTGAAGCATGTTTTAATTGGATAGGGCCTACAG

100 CAGTATTCACCCTTCCTCCGCTCCTGACCTGATATAGGTCTATGTGCGGG

150 AAAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAAGGC

Total 200: {:A=>52, :C=>51, :G=>49, :T=>48}

0 TAAGCTGAGGTGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA

50 CTCACCCATACTCGCTCTGAAGCATGTTTTAATTGGATAGGGCCTACAGC

100 AGTATTCACCCTTCCTCCGCTCCTGACCTGATATAGGTCTATGTGCGGGA

150 AAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAAGGC

Total 199: {:A=>52, :C=>50, :G=>49, :T=>48}