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add unit tests

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This commit is contained in:
Arthur Lu
2024-05-28 19:40:16 +00:00
parent 685f43c19b
commit d04679819d
8 changed files with 1641 additions and 66 deletions
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package.json
+3 -3
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@@ -4,15 +4,15 @@
"description": "Wavefront alignment algorithm in JS",
"main": "src/main.js",
"type": "module",
"dependencies": {},
"devDependencies": {
"eslint": "^8.43.0",
"eslint-config-standard": "^17.1.0",
"eslint-plugin-import": "^2.27.5",
"eslint-plugin-n": "^16.0.1",
"eslint-plugin-promise": "^6.1.1"
"eslint-plugin-promise": "^6.1.1",
"progress": "^2.0.3"
},
"scripts": {
"lint": "DEBUG=eslint:cli-engine eslint --fix ."
}
}
}
src/main.js
+28 -11
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@@ -1,14 +1,31 @@
import wf_align from "./wfa.js";
import fs from "fs";
import ProgressBar from "progress";
const p = {
x: 4,
o: 6,
e: 2
};
let data = fs.readFileSync("./tests/tests.json");
data = JSON.parse(data);
const sequences = fs.readFileSync("./tests/sequences").toString().split("\n");
//const total = sequences.length;
const total = 500; // skip the later tests because of memory usage
// this should be score=24, Alignment=XDIX
console.time("time")
const {CIGAR, score} = wf_align("TCTTTACTCGCGCGTTGGAGAAATACAATAGT", "TCTATACTGCGCGTTTGGAGAAATAAAATAGT", p)
console.timeEnd("time")
console.log(`score: ${score}`);
console.log(`CIGAR: ${CIGAR}`);
for (const test_name of Object.keys(data)) {
const test = data[test_name];
const penalties = test.penalties;
const solutions = fs.readFileSync(test.solutions).toString().split("\n");
const bar = new ProgressBar(":bar :current/:total", { total: total / 2 });
console.log(`test: ${test_name}`);
let correct = 0;
let j = 0;
for (let i = 0; i < total; i += 2) {
const s1 = sequences[i].replace(">");
const s2 = sequences[i + 1].replace("<");
const { CIGAR, score } = wf_align(s1, s2, penalties);
const solution_score = Number(solutions[j].split("\t")[0]);
if (solution_score === -score) {
correct += 1;
}
j += 1;
bar.tick();
}
console.log(`correct: ${correct}\ntotal: ${total / 2}\n`);
}
src/wfa.js
+56 -52
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@@ -5,6 +5,7 @@ class WavefrontComponent {
this.W = []; // wavefront diag distance for each wavefront
this.A = []; // compact CIGAR for backtrace
}
// get value for wavefront=score, diag=k
get_val (score, k) {
if (this.W[score] !== undefined && this.W[score][k] !== undefined) {
@@ -14,6 +15,7 @@ class WavefrontComponent {
return NaN;
}
}
// set value for wavefront=score, diag=k
set_val (score, k, val) {
if (this.W[score]) {
@@ -24,7 +26,8 @@ class WavefrontComponent {
this.W[score][k] = val;
}
}
// get alignment traceback
// get alignment traceback
get_traceback (score, k) {
if (this.A[score] !== undefined && this.A[score][k] !== undefined) {
return this.A[score][k];
@@ -33,6 +36,7 @@ class WavefrontComponent {
return undefined;
}
}
// set alignment traceback
set_traceback (score, k, traceback) {
if (this.A[score]) {
@@ -43,24 +47,29 @@ class WavefrontComponent {
this.A[score][k] = traceback;
}
}
// get hi for wavefront=score
get_hi (score) {
const hi = this.hi[score];
return isNaN(hi) ? 0 : hi;
}
// set hi for wavefront=score
set_hi (score, hi) {
this.hi[score] = hi;
}
// get lo for wavefront=score
get_lo (score) {
const lo = this.lo[score];
return isNaN(lo) ? 0 : lo;
}
// set lo for wavefront=score
set_lo (score, lo) {
this.lo[score] = lo;
}
// string representation of all wavefronts
toString () {
const traceback_str = ["OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"];
@@ -85,7 +94,7 @@ class WavefrontComponent {
s += "|";
}
}
s += ">\t<"
s += ">\t<";
for (let k = min_lo; k <= max_hi; k++) {
s += FormatNumberLength(k, 2);
if (k < max_hi) {
@@ -143,8 +152,8 @@ const traceback = {
Sub: 4,
Ins: 5,
Del: 6,
End: 7,
}
End: 7
};
function FormatNumberLength (num, length) {
let r = "" + num;
@@ -170,13 +179,8 @@ function max (args) {
return max === -Infinity ? NaN : max;
}
function argmin (args) {
const val = min(args)
return args.indexOf(val);
}
function argmax (args) {
const val = max(args)
const val = max(args);
return args.indexOf(val);
}
@@ -190,7 +194,7 @@ export default function wf_align (s1, s2, penalties) {
M.set_val(0, 0, 0);
M.set_hi(0, 0);
M.set_lo(0, 0);
M.set_traceback(0, 0, traceback.End)
M.set_traceback(0, 0, traceback.End);
const I = new WavefrontComponent();
const D = new WavefrontComponent();
while (true) {
@@ -244,7 +248,7 @@ function wf_next (M, I, D, score, penalties) {
I.set_traceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
M.get_val(score - o - e, k - 1),
I.get_val(score - e, k - 1)
])])
])]);
D.set_val(score, k, max([
M.get_val(score - o - e, k + 1),
D.get_val(score - e, k + 1)
@@ -252,7 +256,7 @@ function wf_next (M, I, D, score, penalties) {
D.set_traceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
M.get_val(score - o - e, k + 1),
D.get_val(score - e, k + 1)
])])
])]);
M.set_val(score, k, max([
M.get_val(score - x, k) + 1,
I.get_val(score, k),
@@ -279,46 +283,46 @@ function wf_backtrace (M, I, D, score, penalties, A_k) {
while (!done) {
CIGAR_rev += traceback_CIGAR[current_traceback];
switch (current_traceback) {
case traceback.OpenIns:
tb_s = tb_s - o - e;
tb_k = tb_k - 1;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.ExtdIns:
tb_s = tb_s - e;
tb_k = tb_k - 1;
current_traceback = I.get_traceback(tb_s, tb_k);
break;
case traceback.OpenDel:
tb_s = tb_s - o - e;
tb_k = tb_k + 1;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.ExtdDel:
tb_s = tb_s - e;
tb_k = tb_k + 1;
current_traceback = D.get_traceback(tb_s, tb_k);
break;
case traceback.Sub:
tb_s = tb_s - x;
tb_k = tb_k;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.Ins:
tb_s = tb_s;
tb_k = tb_k;
current_traceback = I.get_traceback(tb_s, tb_k);
break;
case traceback.Del:
tb_s = tb_s;
tb_k = tb_k;
current_traceback = D.get_traceback(tb_s, tb_k)
break;
case traceback.End:
done = true
break;
case traceback.OpenIns:
tb_s = tb_s - o - e;
tb_k = tb_k - 1;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.ExtdIns:
tb_s = tb_s - e;
tb_k = tb_k - 1;
current_traceback = I.get_traceback(tb_s, tb_k);
break;
case traceback.OpenDel:
tb_s = tb_s - o - e;
tb_k = tb_k + 1;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.ExtdDel:
tb_s = tb_s - e;
tb_k = tb_k + 1;
current_traceback = D.get_traceback(tb_s, tb_k);
break;
case traceback.Sub:
tb_s = tb_s - x;
// tb_k = tb_k;
current_traceback = M.get_traceback(tb_s, tb_k);
break;
case traceback.Ins:
// tb_s = tb_s;
// tb_k = tb_k;
current_traceback = I.get_traceback(tb_s, tb_k);
break;
case traceback.Del:
// tb_s = tb_s;
// tb_k = tb_k;
current_traceback = D.get_traceback(tb_s, tb_k);
break;
case traceback.End:
done = true;
break;
}
}
const CIGAR = Array.from(CIGAR_rev).reverse().join("");
return {CIGAR, score};
return { CIGAR, score };
}
tests/sequences
+610
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tests/test_affine_p0_sol
+305
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tests/test_affine_p1_sol
+305
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tests/test_affine_p2_sol
+305
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tests/tests.json
+29
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@@ -0,0 +1,29 @@
{
"p0": {
"penalties": {
"m": 0,
"x": 1,
"o": 2,
"e": 1
},
"solutions": "./tests/test_affine_p0_sol"
},
"p1": {
"penalties": {
"m": 0,
"x": 3,
"o": 1,
"e": 4
},
"solutions": "./tests/test_affine_p1_sol"
},
"p2": {
"penalties": {
"m": 0,
"x": 5,
"o": 3,
"e": 2
},
"solutions": "./tests/test_affine_p2_sol"
}
}