Bioinformatics/Sequence mutation: Difference between revisions

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);