nucleotide - npm Package Compare versions

Comparing version 0.9.1 to 0.12.0

package.json

@@ -23,6 +23,7 @@ {
   },
-  "version": "0.9.1",
+  "version": "0.12.0",
   "devDependencies": {
-    "mf-parser": "^0.9.1"
-  }
+    "mf-parser": "^0.12.0"
+  },
+  "gitHead": "aa2e6571c5f7121dda616b7d6920b7a653a8f9c7"
 }

src/__tests__/furanThreeTerm.test.js

@@ -7,5 +7,20 @@ 'use strict';
   it('remove base of three terminal of HDampDtmpDcmp', () => {
-    let modified = furanThreeTerm('HDampDtmpDcmp', { a: true });
+    let modified = furanThreeTerm('HDampDtmpDcmp');
     expect(modified).toBe('HDampDtmpC5H6O4P');
   });
+
+  it('remove base of three terminal of HDamp', () => {
+    let modified = furanThreeTerm('HDamp');
+    expect(modified).toBe('HC5H6O4P');
+  });
+
+  it('remove base of three terminal of (C5H3)DampDtmp', () => {
+    let modified = furanThreeTerm('(C5H3)DampDtmp');
+    expect(modified).toBe('(C5H3)DampC5H6O4P');
+  });
+
+  it('remove base of three terminal of HODamp', () => {
+    let modified = furanThreeTerm('HODamp');
+    expect(modified).toBe('HOC5H6O4P');
+  });
 });

src/__tests__/generateFragments.test.js

@@ -6,11 +6,31 @@ 'use strict';
 describe('test generate fragments', () => {
-  it('nucleotide to sequence of OHDampDtmpDcmpH', () => {
+  it('nucleotide to sequence of HODampDtmpDcmpH', () => {
     let fragments = generateFragments('HODampDtmpDcmpH', { a: true });
-    expect(fragments).toMatchSnapshot();
+    expect(fragments).toStrictEqual(['HODampO-1H-1$a1', 'HODampDtmpO-1H-1$a2']);
   });
-  it('nucleotide to sequence of HODampDtmpDcmpH', () => {
+
+  it('nucleotide to sequence internal modification of HODamp(NH2)DtmpDcmpH', () => {
+    let fragments = generateFragments('HODamp(NH2)DtmpDcmpH', { a: true });
+    expect(fragments).toStrictEqual([
+      'HODamp(NH2)O-1H-1$a1',
+      'HODamp(NH2)DtmpO-1H-1$a2',
+    ]);
+  });
+
+  it('nucleotide to sequence HODampDtmpDcmpH', () => {
     let fragments = generateFragments('HODampDtmpDcmpH', { a: true, ab: true });
-    expect(fragments).toMatchSnapshot();
+    expect(fragments).toStrictEqual([
+      'HODampO-1H-1$a1',
+      'HODampDtmpO-1H-1$a2',
+      'HODampC5H6O4P$a2-B',
+    ]);
   });
 
+  it('nucleotide HODampDtmpDcmpH dh2o (d with loss of water)', () => {
+    let fragments = generateFragments('HODampDampH', {
+      dh2o: true,
+    });
+    expect(fragments).toStrictEqual(['HODampPO2$d-H2O1']);
+  });
+
   it('nucleotide to sequence of HODampDtmpDcmpH and many fragments', () => {
@@ -26,6 +46,24 @@ let fragments = generateFragments('HODampDtmpDcmpH', {
       y: true,
-      z: true
+      z: true,
     });
-    expect(fragments).toMatchSnapshot();
+    expect(fragments).toStrictEqual([
+      'HODampO-1H-1$a1',
+      'HODampH$b1',
+      'HODampPO2$c1',
+      'HODampPO3H2$d1',
+      'HODcmpH$w1',
+      'H-1DcmpH$x1',
+      'O-2P-1DcmpH$y1',
+      'O-3H-2P-1DcmpH$z1',
+      'HODampDtmpO-1H-1$a2',
+      'HODampC5H6O4P$a2-B',
+      'HODampDtmpH$b2',
+      'HODampDtmpPO2$c2',
+      'HODampDtmpPO3H2$d2',
+      'HODtmpDcmpH$w2',
+      'H-1DtmpDcmpH$x2',
+      'O-2P-1DtmpDcmpH$y2',
+      'O-3H-2P-1DtmpDcmpH$z2',
+    ]);
   });
 });

src/__tests__/nucleotide.test.js

@@ -8,2 +8,16 @@ 'use strict';
 describe('test nucleotide', () => {
+  it('nucleotide to sequence of emtpy string', () => {
+    let sequence = Nucleotide.sequenceToMF(' ');
+    expect(sequence).toStrictEqual('');
+    let mass = new MF(sequence).getInfo().mass;
+    expect(mass).toBeCloseTo(0, 1);
+  });
+
+  it('nucleotide to sequence of atc', () => {
+    let sequence = Nucleotide.sequenceToMF('atc');
+    expect(sequence).toStrictEqual('HODampDtmpDcmpH.HODgmpDampDtmpH');
+    let mass = new MF(sequence).getInfo().mass;
+    expect(mass).toBeCloseTo(1889.23, 1);
+  });
+
   it('nucleotide to sequence of ATC', () => {
@@ -15,3 +29,17 @@ let sequence = Nucleotide.sequenceToMF('ATC');
   });
+  it('nucleotide to sequence of A(H-1C-1)TC', () => {
+    let sequence = Nucleotide.sequenceToMF('A(H-1C-1)TC', { kind: 'dna' });
+    expect(sequence).toStrictEqual('HODamp(H-1C-1)DtmpDcmpH');
+  });
 
+  it('nucleotide to sequence of (HO)ATC(NH2)', () => {
+    let sequence = Nucleotide.sequenceToMF('(HO)ATC(NH2)', { kind: 'dna' });
+    expect(sequence).toStrictEqual('(HO)DampDtmpDcmp(NH2)');
+  });
+
+  it('nucleotide to sequence of (HO)atc(NH2)', () => {
+    let sequence = Nucleotide.sequenceToMF('(HO)atc(NH2)', { kind: 'dna' });
+    expect(sequence).toStrictEqual('(HO)DampDtmpDcmp(NH2)');
+  });
+
   it('nucleotide to sequence of AAU ', () => {
@@ -45,6 +73,6 @@ let sequence = Nucleotide.sequenceToMF('AAU');
 
-  it('nucleotide to sequence of DNA AAA with 5\' alcohol', () => {
+  it("nucleotide to sequence of DNA AAA with 5' alcohol", () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
       fivePrime: 'alcohol',
-      kind: 'DNA'
+      kind: 'DNA',
     });
@@ -56,6 +84,6 @@ expect(sequence).toStrictEqual('HODadeDampDampH');
 
-  it('nucleotide to sequence of DNA AAA with 5\' monophosphate', () => {
+  it("nucleotide to sequence of DNA AAA with 5' monophosphate", () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
       fivePrime: 'monophosphate',
-      kind: 'DNA'
+      kind: 'DNA',
     });
@@ -66,6 +94,6 @@ expect(sequence).toStrictEqual('HODampDampDampH');
   });
-  it('nucleotide to sequence of DNA AAA with 5\' diphosphate', () => {
+  it("nucleotide to sequence of DNA AAA with 5' diphosphate", () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
       fivePrime: 'diphosphate',
-      kind: 'DNA'
+      kind: 'DNA',
     });
@@ -77,6 +105,6 @@ expect(sequence).toStrictEqual('HODadpDampDampH');
 
-  it('nucleotide to sequence of DNA AAA with 5\' triphosphate', () => {
+  it("nucleotide to sequence of DNA AAA with 5' triphosphate", () => {
     let sequence = Nucleotide.sequenceToMF('AAA', {
       fivePrime: 'triphosphate',
-      kind: 'DNA'
+      kind: 'DNA',
     });
@@ -83,0 +111,0 @@ expect(sequence).toStrictEqual('HODatpDampDampH');

src/furanThreeTerm.js

@@ -7,6 +7,6 @@ 'use strict';
     .replace(/ /g, '')
-    .replace(/([a-zA-Z0-9)])([A-Z])/g, '$1 $2')
+    .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
   let last = parts.pop();
-  if (!last.match(/^D[atcg]mp/)) {
+  if (!last.match(/D[atcg]mp(.*)$/)) {
     // eslint-disable-next-line no-console
@@ -16,6 +16,7 @@ console.warn(
     );
+    return parts.join('') + last;
   }
-  return `${parts.join('')}C5H6O4P`;
+  return parts.join('') + last.replace(/D[atcg]mp(.*)$/, 'C5H6O4P');
 }
 
 module.exports = furanThreeTerm;

src/generateFragments.js

 'use strict';
 
-const furanThreeTerm = require('./furanThreeTerm');
+const addInternalTerm = require('./addInternalTerm');
+const addFiveTerm = require('./addFiveTerm');
+const addFiveTermBaseLoss = require('./addFiveTermBaseLoss');
+const addThreeTerm = require('./addThreeTerm');
+const addThreeTermBaseLoss = require('./addThreeTermBaseLoss');
 
-module.exports = function (mf, options) {
+module.exports = function generateFragments(mf, options) {
   if (options === undefined) {
@@ -13,27 +17,44 @@ options = {
       d: false,
+      dh2o: false,
       w: false,
       x: false,
       y: false,
-      z: false
+      z: false,
+      zch2: false,
+      aw: false,
+      bw: false,
+      abw: false,
+      aby: false,
+      abcdBaseLoss: false,
+      wxyzBaseLoss: false
     };
   }
 
-  var mfs = [];
+  let mfs = [];
   // need to allow 0-9 to deal with neutral loss
-  var mfparts = mf
+  let mfparts = mf
     .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
 
-  var fiveTerm = '';
-  var threeTerm = '';
+  let fiveTerm = '';
+  let threeTerm = '';
 
-  for (var i = 1; i < mfparts.length; i++) {
-    fiveTerm += mfparts[i - 1];
-    threeTerm = mfparts[mfparts.length - i] + threeTerm;
-    addFiveTerm(mfs, fiveTerm, i, options);
-    addThreeTerm(mfs, threeTerm, i, options);
+  for (let ter5 = 1; ter5 < mfparts.length; ter5++) {
+    fiveTerm += mfparts[ter5 - 1];
+    threeTerm = mfparts[mfparts.length - ter5] + threeTerm;
+
+    addFiveTerm(mfs, fiveTerm, ter5, options);
+    addFiveTermBaseLoss(mfs, fiveTerm, ter5, options);
+    addThreeTerm(mfs, threeTerm, ter5, options);
+    addThreeTermBaseLoss(mfs, threeTerm, ter5, options);
   }
 
-  if (mfs.length === 0) {
-    mfs = mfs.concat([mf]);
+  for (let i = 1; i < mfparts.length - 1; i++) {
+    let internal = '';
+    for (let j = i; j < mfparts.length - 1; j++) {
+      internal += mfparts[j];
+      if (j > i) {
+        addInternalTerm(mfs, internal, mfparts.length - i, j + 1, options);
+      }
+    }
   }
@@ -43,16 +64,1 @@
 };
-
-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${i}`);
-}
-
-function addThreeTerm(mfs, threeTerm, i, options) {
-  if (options.w) mfs.push(`O${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}`);
-}

src/index.js

@@ -13,6 +13,10 @@ 'use strict';
 function sequenceToMF(sequence, options = {}) {
+  let fivePrimeTerminal = 'HO';
+  let threePrimeTerminal = 'H';
+  sequence = sequence.trim();
+
+  if (sequence === '') return '';
   let { kind, circular, fivePrime = 'monophosphate' } = options;
   fivePrime = fivePrime.replace(/[^a-zA-Z]/g, '').toLowerCase();
 
-  sequence = sequence.toUpperCase().replace(/[^ATCGU]/g, '');
   if (!kind) {
@@ -28,20 +32,59 @@ if (sequence.includes('U')) {
 
+  if (sequence.includes('(') && kind === 'dsdna') {
+    throw new Error(
+      'Nucleotide sequenceToMF: modifications not allowed for ds-DNA'
+    );
+  }
+
   let results = [[]];
   if (kind === 'dsdna') results.push([]);
 
+  let parenthesisCounter = 0;
+
   for (let i = 0; i < sequence.length; i++) {
-    let nucleotide = sequence[i];
+    let currentSymbol = sequence[i];
+
+    if (
+      currentSymbol === '(' ||
+      currentSymbol === ')' ||
+      parenthesisCounter > 0
+    ) {
+      if (currentSymbol === '(') {
+        parenthesisCounter++;
+        if (i === 0) fivePrimeTerminal = '';
+      }
+      if (currentSymbol === ')') {
+        parenthesisCounter--;
+        if (i === sequence.length - 1) threePrimeTerminal = '';
+      }
+      switch (kind) {
+        case 'dna':
+        case 'rna':
+          results[0].push(currentSymbol);
+          break;
+        default:
+          // eslint-disable-next-line no-console
+          console.warn(
+            `Nucleotide sequenceToMF with modification: unknown kind: ${kind}`
+          );
+      }
+      continue;
+    }
+
     let nucleotideType = i === 0 ? fivePrime : 'monophosphate';
 
+    currentSymbol = currentSymbol.toUpperCase().replace(/[^ATCGU]/, '');
+    if (!currentSymbol) continue;
+
     switch (kind) {
       case 'dna':
-        results[0].push(desoxyNucleotides[nucleotideType][nucleotide]);
+        results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]);
         break;
       case 'rna':
-        results[0].push(oxyNucleotides[nucleotideType][nucleotide]);
+        results[0].push(oxyNucleotides[nucleotideType][currentSymbol]);
         break;
       case 'dsdna':
-        results[0].push(desoxyNucleotides[nucleotideType][nucleotide]);
+        results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]);
         results[1].unshift(
-          desoxyNucleotides[nucleotideType][complementary[nucleotide]]
+          desoxyNucleotides[nucleotideType][complementary[currentSymbol]]
         );
@@ -56,4 +99,4 @@ break;
   if (!circular) {
-    results.forEach((result) => result.unshift('HO'));
-    results.forEach((result) => result.push('H'));
+    results.forEach((result) => result.unshift(fivePrimeTerminal));
+    results.forEach((result) => result.push(threePrimeTerminal));
   }
@@ -67,3 +110,4 @@
   generateFragments: require('./generateFragments'),
-  furanThreeTerm: require('./furanThreeTerm')
+  furanThreeTerm: require('./furanThreeTerm'),
+  baseLoss: require('./baseLoss')
 };
@@ -70,0 +114,0 @@

New alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

25516

increased by117.03%

Number of package files

20

increased by100%

Lines of code

652

increased by124.83%

Worsened metrics

Number of medium supply chain risk alerts

1

increased byInfinity%

No dependency changes