Shuffle

Evan Senter

Altschul, S. F., & Erickson, B. W. (1985). Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Molecular biology and evolution, 2(6), 526–38. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3870875

shuffler = Shuffle.new("AGACATAAAGTTCCGTACTGCCGGGAT")
puts (dishuffled_sequence = shuffler.dishuffle)
#=> AGAAGTACAATCGGTACGATTGGCCCT
shuffler.valid?(dishuffled_sequence, 2)
#=> true (Shuffler preserved the di-token frequency)
shuffler.valid?(dishuffled_sequence, 3)
#=> false-ish (Shuffler does not guarantee to preserve the tri-token frequency)
puts (trishuffled_sequence = shuffler.shuffle(3))
#=> AGTACTGCCGTTCCGGGATAAAGACAT
shuffler.valid?(trishuffled_sequence, 3)
#=> true

motivation.