Bioinformatics/Sequence mutation: Difference between revisions

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=={{header|JavaScript}}==

<lang javascript>// Basic set-up

const numBases = 250

const numMutations = 30

const bases = ['A', 'C', 'G', 'T'];

// Utility functions

const copy = arr => [...arr];

const randTo = max => () => (Math.random() * max) | 0;

const randBasePos = randTo(bases.length);

const randBase = () => bases[randBasePos()];

const leftPadN = n => v => {

const arr = [...('' + v)];

const short = n - arr.length;

return short ? [...(Array(short).fill(' ')), ...arr].join('') : arr.join('');

}

const filterCount = arr => s => arr.filter(e => e === s).length;

// Pretty Print functions

const prettyPrint = seq => {

let idx = 0;

const pad = leftPadN(4);

const print = (v, s) => console.log(`${pad(v)}:\t${s}`)

const rem = seq.reduce((p,c) => {

const s = p + c;

if (s.length === 50) {

print(idx, s);

idx = idx + 50;

return '';

}

return s;

}, '');

if (rem !== '') {

print(idx, rem);

}

}

const printBases = seq => {

const filterSeq = filterCount(seq);

const pad = leftPadN(4);

const print = (v, n) => console.log(`${pad(v)}:\t${n}`)

let tot = 0;

bases.forEach(e => {

const cnt = filterSeq(e);

print(e, cnt);

tot = tot + cnt;

})

print('Σ', tot);

}

const select = seq => {

const randPos = randTo(seq.length)();

const extBase = seq[randPos];

const newBase = randBase();

return [randPos, extBase, newBase];

}

// Mutations definitions

const swap = ([hist, seq]) => {

const arr = copy(seq);

const [randPos, extBase, newBase] = select(arr);

arr.splice(randPos, 1, newBase);

const opp = `Swapped ${extBase} for ${newBase} at ${randPos}`;

return [[...hist, opp], arr];

};

const del = ([hist, seq]) => {

const arr = copy(seq);

const [randPos, extBase, _] = select(arr);

const opp = `Deleted ${extBase} at ${randPos}`;

arr.splice(randPos, 1);

return [[...hist, opp], arr];

}

const insert = ([hist, seq]) => {

const arr = copy(seq);

const [randPos, _, newBase] = select(arr);

const opp = `Inserted ${newBase} at ${randPos}`;

arr.splice(randPos, 0, newBase);

return [[...hist, opp], arr];

}

// Create the starting sequence

const seq = Array(numBases).fill(undefined).map(randBase);

// Create a set of mutations

const operations = [swap, del, insert];

const randMutate = randTo(operations.length);

const randomMutation = () => operations[randMutate()];

const mutations = Array(numMutations).fill(undefined).map(randomMutation);

// Mutate the sequence

const [hist, mut] = mutations.reduce((p,c,i) => c(p), [[], seq]);

console.log('ORIGINAL SEQUENCE:')

prettyPrint(seq);

console.log('\nBASE COUNTS:')

printBases(seq);

console.log('\nMUTATION LOG:')

hist.forEach((e,i) => console.log(`${i}:\t${e}`));

console.log('\nMUTATED SEQUENCE:')

prettyPrint(mut);

console.log('\nMUTATED BASE COUNTS:')

printBases(mut);

</lang>

{{out}}

<pre>

ORIGINAL SEQUENCE:

0: CATTGTGAACCGGAATTATAGTTATACCGAAGATGCCAGAGTCCGGGGGA

50: GCGGATGCAGGGTATGTTCCTCAGAACCCCGTCATGCACGGCCTATACGG

100: AAAGGAAGGGCCTGCGCAGACTTAAGACAAGGAGGACTGTATGAAAGGGA

150: TGGCTTGTGTGGGAAGAGCACCGCGCGCGAAGCCTGTAATCGACTACAGC

200: AAATAATTATGTTGATACGGCAAATGGTCATAATCGCCCCCACCCGCGGT

BASE COUNTS:

A: 70

C: 57

G: 75

T: 48

Σ: 250

MUTATION LOG:

0: Swapped G for T at 53

1: Swapped G for A at 174

2: Inserted A at 105

3: Inserted G at 136

4: Swapped G for C at 183

5: Swapped T for A at 188

6: Deleted C at 240

7: Inserted G at 62

8: Deleted A at 166

9: Deleted G at 215

10: Inserted A at 130

11: Inserted G at 174

12: Deleted G at 162

13: Swapped A for A at 1

14: Swapped G for G at 117

15: Deleted C at 140

16: Inserted C at 217

17: Inserted C at 220

18: Inserted A at 150

19: Swapped T for T at 206

20: Inserted G at 153

21: Deleted T at 33

22: Deleted A at 190

23: Deleted A at 120

24: Deleted A at 141

25: Deleted T at 206

26: Inserted C at 216

27: Deleted G at 110

28: Inserted G at 230

29: Deleted G at 43

MUTATED SEQUENCE:

0: CATTGTGAACCGGAATTATAGTTATACCGAAGAGCCAGAGTCCGGGGAGC

50: GTATGCAGGGGTATGTTCCTCAGAACCCCGTCATGCACGGCCTATACGGA

100: AAGGAAAGGCCTGCGCAGCTTAAGACAAAGGAGGGATGTTGAAAGAGGGA

150: TGGCTTGTTGGGAGAGCACGCGCACGCGAACCCTGAATCGACTACAGCAA

200: ATAATATGTTATCACCCGGCAAATGGTCAGTAATCGCCCCACCCGCGGT

MUTATED BASE COUNTS:

A: 71

C: 59

G: 73

T: 46

Σ: 249