Wobble Hypothesis - Combination or Permutation of Array of strings in ruby

Question

I have a ruby array with 4 strings

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

I need 4^3 combinations of strings.

new_array = ['AGC', 'AGT' .. 'TTT']

This is the wobble hypothesis in genetics. Could someone explain how I could go about achieving this using ruby.

Its based on amino acid triplet codons. so 'UUU', 'UUC' code for Phenyl alanine and so forth. — Stacked-for-life, Aug 26 '14 at 15:29

score 5 · Answer 1 · answered Aug 26 '14 at 15:27

5

use Array#repeated_permutation:

nucleotides = %w(A G C T)
nucleotides.repeated_permutation(3).map(&:join)
#=> ["AAA", "AAG", "AAC", "AAT", "AGA", "AGG", "AGC", "AGT", "ACA", "ACG", "ACC", "ACT", "ATA", "ATG", "ATC", "ATT", "GAA", "GAG", "GAC", "GAT", "GGA", "GGG", "GGC", "GGT", "GCA", "GCG", "GCC", "GCT", "GTA", "GTG", "GTC", "GTT", "CAA", "CAG", "CAC", "CAT", "CGA", "CGG", "CGC", "CGT", "CCA", "CCG", "CCC", "CCT", "CTA", "CTG", "CTC", "CTT", "TAA", "TAG", "TAC", "TAT", "TGA", "TGG", "TGC", "TGT", "TCA", "TCG", "TCC", "TCT", "TTA", "TTG", "TTC", "TTT"]

answered Aug 26 '14 at 15:27

Stefan

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Ha! Didn't know about this one – fl00r Aug 26 '14 at 15:28
This does not work in 1.8.7 but yea would be very useful once we upgrade. Thank you – Stacked-for-life Aug 26 '14 at 15:35

score 3 · Accepted Answer · answered Aug 26 '14 at 15:15

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nucleotides = ['A', 'G', 'C', 'T'] 
(nucleotides*3).permutation(3).to_a.map(&:join).uniq
#=> ["AGC", "AGT", "AGA", "AGG", "ACG", "ACT", "ACA", "ACC", "ATG", "ATC", "ATA", "ATT", "AAG", "AAC", "AAT", "AAA", "GAC", "GAT", "GAA", "GAG", "GCA", "GCT", "GCG", "GCC", "GTA", "GTC", "GTG", "GTT", "GGA", "GGC", "GGT", "GGG", "CAG", "CAT", "CAA", "CAC", "CGA", "CGT", "CGG", "CGC", "CTA", "CTG", "CTC", "CTT", "CCA", "CCG", "CCT", "CCC", "TAG", "TAC", "TAA", "TAT", "TGA", "TGC", "TGG", "TGT", "TCA", "TCG", "TCC", "TCT", "TTA", "TTG", "TTC", "TTT"]

answered Aug 26 '14 at 15:15

fl00r

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is `ACG` valid? Or only `AGC`? – fl00r Aug 26 '14 at 15:19
well this does not give me all 64 right. permutation does not give 'AAA' and such repetetions – Stacked-for-life Aug 26 '14 at 15:22
1

@Stacked-for-life, actually it does :) `(nucleotides*3).permutation(3).to_a.map(&:join).uniq.include?("AAA") #=> true` – fl00r Aug 26 '14 at 15:25
1

And: `(nucleotides*3).permutation(3).to_a.map(&:join).uniq.size #=> 64` – fl00r Aug 26 '14 at 15:26
Awesome I did not see the multiplier. This works in ruby 1.8.7 too – Stacked-for-life Aug 26 '14 at 15:30
@Stefan's answer would be more appropriable :) – fl00r Aug 26 '14 at 15:33

score 0 · Answer 3 · answered Aug 26 '14 at 15:28

0

Ruby has the basic combinatorial enumerators baked in. Array#repeated_permutation should produce the desired result:

nucleotides.repeated_permutation(3).map(&:join)
#=> ["AAA", "AAG", ..., "TTT"]

answered Aug 26 '14 at 15:28

Patrick Oscity

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Wobble Hypothesis - Combination or Permutation of Array of strings in ruby

3 Answers3