nucleotide - npm Package Compare versions

Comparing version 0.8.0 to 0.9.1

package.json

@@ -23,6 +23,6 @@ {
   },
-  "version": "0.8.0",
+  "version": "0.9.1",
   "devDependencies": {
-    "mf-parser": "^0.8.0"
+    "mf-parser": "^0.9.1"
   }
 }

src/__tests__/furanThreeTerm.test.js

 'use strict';
 
 const { furanThreeTerm } = require('..');
-const MF = require('mf-parser').MF;
 
 describe('test nucleotide', () => {
-  test('remove base of three terminal of HDampDtmpDcmp', () => {
+  it('remove base of three terminal of HDampDtmpDcmp', () => {
     let modified = furanThreeTerm('HDampDtmpDcmp', { a: true });
@@ -9,0 +8,0 @@ expect(modified).toBe('HDampDtmpC5H6O4P');

src/__tests__/generateFragments.test.js

@@ -6,6 +6,7 @@ 'use strict';
 describe('test generate fragments', () => {
-  test('nucleotide to sequence of OHDampDtmpDcmpH', () => {
+  it('nucleotide to sequence of OHDampDtmpDcmpH', () => {
     let fragments = generateFragments('HODampDtmpDcmpH', { a: true });
+    expect(fragments).toMatchSnapshot();
   });
-  test('nucleotide to sequence of HODampDtmpDcmpH', () => {
+  it('nucleotide to sequence of HODampDtmpDcmpH', () => {
     let fragments = generateFragments('HODampDtmpDcmpH', { a: true, ab: true });
@@ -15,3 +16,3 @@ expect(fragments).toMatchSnapshot();
 
-  test('nucleotide to sequence of HODampDtmpDcmpH', () => {
+  it('nucleotide to sequence of HODampDtmpDcmpH and many fragments', () => {
     let fragments = generateFragments('HODampDtmpDcmpH', {
@@ -18,0 +19,0 @@ a: true,

src/__tests__/nucleotide.test.js

 'use strict';
 
 const Nucleotide = require('..');
+
 const MF = require('mf-parser').MF;
 
 describe('test nucleotide', () => {
-  test('nucleotide to sequence of ATC', () => {
+  it('nucleotide to sequence of ATC', () => {
     let sequence = Nucleotide.sequenceToMF('ATC');
-    expect(sequence).toEqual('HODampDtmpDcmpH.HODgmpDampDtmpH');
+    expect(sequence).toStrictEqual('HODampDtmpDcmpH.HODgmpDampDtmpH');
     let mass = new MF(sequence).getInfo().mass;
@@ -14,5 +15,5 @@ expect(mass).toBeCloseTo(1889.23, 1);
 
-  test('nucleotide to sequence of AAU ', () => {
+  it('nucleotide to sequence of AAU ', () => {
     let sequence = Nucleotide.sequenceToMF('AAU');
-    expect(sequence).toEqual('HOAmpAmpUmpH');
+    expect(sequence).toStrictEqual('HOAmpAmpUmpH');
     let mass = new MF(sequence).getInfo().mass;
@@ -22,5 +23,5 @@ expect(mass).toBeCloseTo(982.6, 1);
 
-  test('nucleotide to sequence of circular AAA ', () => {
+  it('nucleotide to sequence of circular AAA ', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { circular: true });
-    expect(sequence).toEqual('DampDampDamp.DtmpDtmpDtmp');
+    expect(sequence).toStrictEqual('DampDampDamp.DtmpDtmpDtmp');
     let mass = new MF(sequence).getInfo().mass;
@@ -30,5 +31,5 @@ expect(mass).toBeCloseTo(1852.21, 1);
 
-  test('nucleotide to sequence of DNA AAA ', () => {
+  it('nucleotide to sequence of DNA AAA ', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { kind: 'DNA' });
-    expect(sequence).toEqual('HODampDampDampH');
+    expect(sequence).toStrictEqual('HODampDampDampH');
     let mass = new MF(sequence).getInfo().mass;
@@ -38,5 +39,5 @@ expect(mass).toBeCloseTo(957.64, 1);
 
-  test('nucleotide to sequence of ds-DNA AAA ', () => {
+  it('nucleotide to sequence of ds-DNA AAA ', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { kind: 'ds-DNA' });
-    expect(sequence).toEqual('HODampDampDampH.HODtmpDtmpDtmpH');
+    expect(sequence).toStrictEqual('HODampDampDampH.HODtmpDtmpDtmpH');
     let mass = new MF(sequence).getInfo().mass;
@@ -46,3 +47,3 @@ expect(mass).toBeCloseTo(1888.24, 1);
 
-  test(`nucleotide to sequence of DNA AAA with 5' alcohol`, () => {
+  it('nucleotide to sequence of DNA AAA with 5\' alcohol', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
@@ -52,3 +53,3 @@ fivePrime: 'alcohol',
     });
-    expect(sequence).toEqual('HODadeDampDampH');
+    expect(sequence).toStrictEqual('HODadeDampDampH');
     let mass = new MF(sequence).getInfo().mass;
@@ -58,3 +59,3 @@ expect(mass).toBeCloseTo(877.66, 1);
 
-  test(`nucleotide to sequence of DNA AAA with 5' monophosphate`, () => {
+  it('nucleotide to sequence of DNA AAA with 5\' monophosphate', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
@@ -64,7 +65,7 @@ fivePrime: 'monophosphate',
     });
-    expect(sequence).toEqual('HODampDampDampH');
+    expect(sequence).toStrictEqual('HODampDampDampH');
     let mass = new MF(sequence).getInfo().mass;
     expect(mass).toBeCloseTo(957.64, 1);
   });
-  test(`nucleotide to sequence of DNA AAA with 5' diphosphate`, () => {
+  it('nucleotide to sequence of DNA AAA with 5\' diphosphate', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
@@ -74,3 +75,3 @@ fivePrime: 'diphosphate',
     });
-    expect(sequence).toEqual('HODadpDampDampH');
+    expect(sequence).toStrictEqual('HODadpDampDampH');
     let mass = new MF(sequence).getInfo().mass;
@@ -80,3 +81,3 @@ expect(mass).toBeCloseTo(1037.62, 1);
 
-  test(`nucleotide to sequence of DNA AAA with 5' triphosphate`, () => {
+  it('nucleotide to sequence of DNA AAA with 5\' triphosphate', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
@@ -86,3 +87,3 @@ fivePrime: 'triphosphate',
     });
-    expect(sequence).toEqual('HODatpDampDampH');
+    expect(sequence).toStrictEqual('HODatpDampDampH');
     let mass = new MF(sequence).getInfo().mass;
@@ -89,0 +90,0 @@ expect(mass).toBeCloseTo(1117.6, 1);

src/furanThreeTerm.js

@@ -7,13 +7,14 @@ 'use strict';
     .replace(/ /g, '')
-    .replace(/([a-zA-Z0-9\)])([A-Z])/g, '$1 $2')
+    .replace(/([a-zA-Z0-9)])([A-Z])/g, '$1 $2')
     .split(/ /);
   let last = parts.pop();
   if (!last.match(/^D[atcg]mp/)) {
+    // eslint-disable-next-line no-console
     console.warn(
-      'furanThreeTerm can not remove a non monophosphate nucleic acid: ' + last
+      `furanThreeTerm can not remove a non monophosphate nucleic acid: ${last}`
     );
   }
-  return parts.join('') + 'C5H6O4P';
+  return `${parts.join('')}C5H6O4P`;
 }
 
 module.exports = furanThreeTerm;

src/generateFragments.js

@@ -5,3 +5,3 @@ 'use strict';
 
-module.exports = function(mf, options) {
+module.exports = function (mf, options) {
   if (options === undefined) {
@@ -24,3 +24,3 @@ options = {
   var mfparts = mf
-    .replace(/([a-z\)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
+    .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
@@ -46,14 +46,14 @@
 function addFiveTerm(mfs, fiveTerm, i, options) {
-  if (options.a) mfs.push(fiveTerm + 'O-1$a' + i);
-  if (options.ab) mfs.push(furanThreeTerm(fiveTerm) + '$a' + i + ' - B');
-  if (options.b) mfs.push(fiveTerm + '$b' + i);
-  if (options.c) mfs.push(fiveTerm + 'PO2H$c' + i);
-  if (options.d) mfs.push(fiveTerm + 'PO3H$d' + i);
+  if (options.a) mfs.push(`${fiveTerm}O-1$a${i}`);
+  if (options.ab) mfs.push(`${furanThreeTerm(fiveTerm)}$a${i} - B`);
+  if (options.b) mfs.push(`${fiveTerm}$b${i}`);
+  if (options.c) mfs.push(`${fiveTerm}PO2H$c${i}`);
+  if (options.d) mfs.push(`${fiveTerm}PO3H$d${i}`);
 }
 
 function addThreeTerm(mfs, threeTerm, i, options) {
-  if (options.w) mfs.push('O' + threeTerm + '$w' + i);
-  if (options.x) mfs.push('' + threeTerm + '$x' + i);
-  if (options.y) mfs.push('O-2H-1P-1' + threeTerm + '$y' + i);
-  if (options.z) mfs.push('O-3H-2P-1' + threeTerm + '$z' + i);
+  if (options.w) mfs.push(`O${threeTerm}$w${i}`);
+  if (options.x) mfs.push(`${threeTerm}$x${i}`);
+  if (options.y) mfs.push(`O-2H-1P-1${threeTerm}$y${i}`);
+  if (options.z) mfs.push(`O-3H-2P-1${threeTerm}$z${i}`);
 }

src/index.js

@@ -48,2 +48,3 @@ 'use strict';
       default:
+        // eslint-disable-next-line no-console
         console.warn(`Nucleotide sequenceToMF: unknown kind: ${kind}`);
@@ -54,7 +55,7 @@ }
   if (!circular) {
-    results.forEach(result => result.unshift('HO'));
-    results.forEach(result => result.push('H'));
+    results.forEach((result) => result.unshift('HO'));
+    results.forEach((result) => result.push('H'));
   }
 
-  return results.map(result => result.join('')).join('.');
+  return results.map((result) => result.join('')).join('.');
 }
@@ -61,0 +62,0 @@

No alert changes

Improved metrics

Total package byte prevSize

11757

increased by2.47%

Lines of code

290

increased by0.69%

No dependency changes