Hi everyone.
I’m tasked with using an existing method, compareDNA, to find the two most related instances of pAequor.
I was able to compare all the DNA strands using my compareDNA method, but I can’t easily identify the two strands with the highest overlap without manually scrolling through the lengthy list of logged comparisons.
Any assistance is much appreciated.
The code in question is at the very bottom, which uses the compareDNA method in the pAequorFactory object.
// Randomly selects a base and return the base ('A','T','C', or 'G')
const returnRandBase = () => {
const dnaBases = ['A', 'T', 'C', 'G'];
return dnaBases[Math.floor(Math.random() * 4)]; //returns random index value between 0 and 3 that is assigned to corresponding dnaBase
};
// Generates an array containing 15 bases to represent a single DNA strand with 15 bases.
const mockUpStrand = () => {
const newStrand = [];
for (let i = 0; i < 15; i++) {
newStrand.push(returnRandBase());
// console.log(newStrand);
}
return newStrand;
};
//Factory function to create objects with two parameters, specimen number and DNA strand
let pAequorFactory = (specimenNum, dna) => {
return {
specimenNum,
dna,
// Method to randomly select a DNA base and revise it to a new base
mutate() {
let randomBase = Math.floor(Math.random() * 15);//Randomly selects one of 15 existing DNA bases to replace
let newBase = returnRandBase(this.dna[randomBase]);//Creates a new DNA base to replace existing one
while (newBase === this.dna[randomBase]) { // Ensures existing dna base and new base are different
randomBase = Math.floor(Math.random() * 15);
newBase = returnRandBase(this.dna[randomBase]);
}
this.dna[randomBase] = newBase;
},
// Method to compare two DNA strands and compute percentage of shared DNA
compareDNA (specimenNum, dna) {
let specimenMatches = 0;
console.log(`Original DNA: ${this.dna}.`);
console.log(`Comparison DNA: ${dna}.`);
for (let i = 0; i < dna.length; i++){
if (dna[i] === this.dna[i]){
specimenMatches++;
} else {
continue;
}
}
console.log(`Specimen #${this.specimenNum} and #${specimenNum} have ${specimenMatches} corresponding DNA matches.`);
let percentOverlap = ((specimenMatches/dna.length) * 100).toFixed(1);
// console.log(`Shared DNA is ${percentOverlap}% of total DNA.`);
},
// Method to evaluate a DNA strand. Strands consisting of at least 60% 'C' and 'G' bases are likely to survive.
willLikelySurvive () {
let basesCG = 0;
this.dna.forEach(element => {
if(element === 'C' || element === 'G'){
basesCG++;
}})
return (basesCG / this.dna.length) >= 0.6;
},
//Returns complementary DNA strand
complementStrand () {
let compStrand = [];
for(let i=0; i < 15; i++) {
switch (this.dna[i]) {
case 'A':
compStrand.push(this.dna[i] = 'T');
break;
case 'T':
compStrand.push(this.dna[i] = 'A');
break;
case 'C':
compStrand.push(this.dna[i] = 'G');
break;
case 'G':
compStrand.push(this.dna[i] = 'C');
break;
}
}
return compStrand;
}
}
}
// Compares randomly generated DNA strand with inputted strand
pAequorFactory(1, mockUpStrand()).compareDNA(2, ['A', 'T', 'C', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'C']);
//Prints true if the DNA will survive (i.e. 60%+ of strands are 'C' and 'G'); otherwise false.
console.log(pAequorFactory(1, mockUpStrand()).willLikelySurvive());
//Creates 30 instances of pAequor that can survive in their natural habitat (i.e. 60%+ of strands are 'C' and 'G')
let pAequor30 = [];
let specimenNum = 1;
while (pAequor30.length < 30) {
let dna = mockUpStrand(); // Generates DNA strand
let survive = pAequorFactory(specimenNum, dna).willLikelySurvive(); //Tests if strand will survive
if (survive) { //Only strands that survive are added to the final array.
pAequor30.push({specimenNum, dna});
specimenNum++;
} else {
continue;
}
}
console.log(pAequor30);
// Prints base DNA and associated complementary DNA
let baseDNA = mockUpStrand();
console.log('Base DNA:');
console.log(baseDNA);
console.log('Complementary DNA:');
console.log(pAequorFactory(2, baseDNA).complementStrand());
// console.log(pAequorFactory(1,pAequor30[0].dna).compareDNA(pAequor30[1]));
//Use .compareDNA() to find the two most related instances of pAequor.
let specNum1;
let specNum2;
let highMatch = 0;
for (let i = 0; i < pAequor30.length-1; i++) { //Loops through 29 strands to avoid comparing DNA #30 with itself.
for (let j = i+1; j < pAequor30.length; j++) { //compares each DNA strand to all other DNA strands
pAequorFactory(pAequor30[i].specimenNum,pAequor30[i].dna).compareDNA(pAequor30[j].specimenNum,pAequor30[j].dna);
if (this.specimenMatches > highMatch) {
highMatch = this.specimenMatches;
console.log(highMatch);
specNum1 = pAequor30[i].specimenNum;
specNum2 = pAequor30[j].specimenNum;
} else {
continue;
}
}
}
console.log(`Specimen #${specNum1} and specimen #${specNum2} have the highest DNA overlap, with ${highMatch} matching pairs`);