Bioinformatics/Sequence mutation: Difference between revisions

=={{header|Swift}}==

<lang swift>let bases: [Character] = ["A", "C", "G", "T"]

enum Action: CaseIterable {

case swap, delete, insert

}

@discardableResult

func mutate(dna: inout String) -> Action {

guard let i = dna.indices.shuffled().first(where: { $0 != dna.endIndex }) else {

fatalError()

}

let action = Action.allCases.randomElement()!

switch action {

case .swap:

dna.replaceSubrange(i..<i, with: [bases.randomElement()!])

case .delete:

dna.remove(at: i)

case .insert:

dna.insert(bases.randomElement()!, at: i)

}

return action

}

var d = ""

for _ in 0..<200 {

d.append(bases.randomElement()!)

}

func printSeq(_ dna: String) {

for startI in stride(from: 0, to: dna.count, by: 50) {

print("\(startI): \(dna.dropFirst(startI).prefix(50))")

}

print()

print("Size: \(dna.count)")

print()

let counts = dna.reduce(into: [:], { $0[$1, default: 0] += 1 })

for (char, count) in counts.sorted(by: { $0.key < $1.key }) {

print("\(char): \(count)")

}

}

printSeq(d)

print()

for _ in 0..<20 {

mutate(dna: &d)

}

printSeq(d)</lang>

{{out}}

<pre>0: CCCTGTTACCCTTAAGTCACAAATCATGATAAGCAGCCTTCGAGCACTTC

50: GTGTCAAGCCTGATTCGAGCGCGCCGGTCATCCTCCGATAGAGCACGGGG

100: ACGCCCGCACTACCCCACTGGCGCTTGGTCGCTGAATAGGGCGCCCTTGG

150: TGGTGGATGGTCTTAAGCTGTCGCAAATCTAGCCCCGACCAAGAGAAGGC

Size: 200

A: 43

C: 62

G: 54

T: 41

0: CCCTGTTACCCTTAAGTCACAAATCATGTATAAAGCAGCCTTCGAGCACT

50: TCGTGTCAAGCCTGATTCGAGCGCGCTAGGGCATCCTCCGTATAAGAGCA

100: CCGGGGACGCCCGCACTTACCACCACTGGCGCTTGGTCGCGAATAGGGGC

150: GCCCTTTGGTGGTGGATTGGTCTTAAGTGTCGCAAATCTAGCCCCCGACC

200: AAGAGAAGGC

Size: 210

A: 47

C: 62

G: 56

T: 45</pre>