nucleotide - npm Package Compare versions

Comparing version 0.6.2 to 0.6.4

package.json

 {
-    "author": {
-        "name": "Luc Patiny"
-    },
-    "bugs": {
-        "url": "https://github.com/cheminfo/molecular-formula/issues"
-    },
-    "bundleDependencies": false,
-    "deprecated": false,
-    "description": "Deal with nucleotides and molecular formula",
-    "main": "src/index.js",
-    "files": [
-        "src"
-    ],
-    "homepage": "https://github.com/cheminfo/molecular-formula/tree/master/packages/nucleotide#readme",
-    "keywords": [],
-    "license": "MIT",
-    "name": "nucleotide",
-    "repository": {
-        "type": "git",
-        "url": "git+https://github.com/cheminfo/molecular-formula.git"
-    },
-    "version": "0.6.2"
+  "author": {
+    "name": "Luc Patiny"
+  },
+  "bugs": {
+    "url": "https://github.com/cheminfo/molecular-formula/issues"
+  },
+  "bundleDependencies": false,
+  "deprecated": false,
+  "description": "Deal with nucleotides and molecular formula",
+  "main": "src/index.js",
+  "files": [
+    "src"
+  ],
+  "homepage": "https://github.com/cheminfo/molecular-formula/tree/master/packages/nucleotide#readme",
+  "keywords": [],
+  "license": "MIT",
+  "name": "nucleotide",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cheminfo/molecular-formula.git"
+  },
+  "version": "0.6.4",
+  "devDependencies": {
+    "mf-parser": "^0.6.4"
+  }
 }

src/index.js

@@ -8,2 +8,3 @@ 'use strict';
  * @param {string} [options.kind] - rna, ds-dna or dna. Default if contains U: rna, otherwise ds-dna
+ * @param {string} [options.fivePrime=monophosphate] - alcohol, monophosphate, diphosphate, triphosphate
  * @param {string} [options.circular=false]
@@ -13,58 +14,71 @@ */
 function sequenceToMF(sequence, options = {}) {
-    let { kind, circular } = options;
-    sequence = sequence.toUpperCase().replace(/[^ATCGU]/g, '');
-    if (!kind) {
-        if (sequence.includes('U')) {
-            kind = 'rna';
-        } else {
-            kind = 'ds-dna';
-        }
+  let { kind, circular, fivePrime = 'monophosphate' } = options;
+  fivePrime = fivePrime.replace(/[^a-zA-Z]/g, '').toLowerCase();
+
+  sequence = sequence.toUpperCase().replace(/[^ATCGU]/g, '');
+  if (!kind) {
+    if (sequence.includes('U')) {
+      kind = 'rna';
+    } else {
+      kind = 'ds-dna';
     }
+  }
 
-    kind = kind.replace(/[^A-Za-z]/g, '').toLowerCase();
+  kind = kind.replace(/[^A-Za-z]/g, '').toLowerCase();
 
-    let results = [[]];
-    if (kind === 'dsdna') results.push([]);
+  let results = [[]];
+  if (kind === 'dsdna') results.push([]);
 
+  for (let i = 0; i < sequence.length; i++) {
+    let nucleotide = sequence[i];
+    let nucleotideType = i === 0 ? fivePrime : 'monophosphate';
+
     switch (kind) {
-        case 'dna':
-            for (let nucleotide of sequence) {
-                results[0].push(desoxyNucleotides[nucleotide]);
-            }
-            break;
-        case 'rna':
-            for (let nucleotide of sequence) {
-                results[0].push(oxyNucleotides[nucleotide]);
-            }
-            break;
-        case 'dsdna':
-            for (let nucleotide of sequence) {
-                results[0].push(oxyNucleotides[nucleotide]);
-                results[1].unshift(oxyNucleotides[complementary[nucleotide]]);
-            }
-            break;
-        default:
-            throw new Error(`Nucleotide sequenceToMF: unknown kind: ${kind}`);
+      case 'dna':
+        results[0].push(desoxyNucleotides[nucleotideType][nucleotide]);
+        break;
+      case 'rna':
+        results[0].push(oxyNucleotides[nucleotideType][nucleotide]);
+        break;
+      case 'dsdna':
+        results[0].push(desoxyNucleotides[nucleotideType][nucleotide]);
+        results[1].unshift(
+          desoxyNucleotides[nucleotideType][complementary[nucleotide]]
+        );
+        break;
+      default:
+        console.warn(`Nucleotide sequenceToMF: unknown kind: ${kind}`);
     }
+  }
 
-    if (!circular) {
-        results.forEach((result) => result.unshift('HO'));
-        results.forEach((result) => result.push('H'));
-    }
+  if (!circular) {
+    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('.');
 }
 
 module.exports = {
-    sequenceToMF
+  sequenceToMF,
+  generateFragments: require('./generateFragments'),
+  furanThreeTerm: require('./furanThreeTerm')
 };
 
 const complementary = {
-    A: 'T',
-    T: 'A',
-    C: 'G',
-    G: 'C'
+  A: 'T',
+  T: 'A',
+  C: 'G',
+  G: 'C'
 };
 
 const desoxyNucleotides = {
+  alcohol: {
+    A: 'Dade',
+    C: 'Dcyt',
+    G: 'Dgua',
+    T: 'Dthy',
+    U: 'Dura'
+  },
+  monophosphate: {
     A: 'Damp',
@@ -75,5 +89,28 @@ C: 'Dcmp',
     U: 'Dump'
+  },
+  diphosphate: {
+    A: 'Dadp',
+    C: 'Dcdp',
+    G: 'Dgdp',
+    T: 'Dtdp',
+    U: 'Dudp'
+  },
+  triphosphate: {
+    A: 'Datp',
+    C: 'Dctp',
+    G: 'Dgtp',
+    T: 'Dttp',
+    U: 'Dutp'
+  }
 };
 
 const oxyNucleotides = {
+  alcohol: {
+    A: 'Ade',
+    C: 'Cyt',
+    G: 'Gua',
+    T: 'Thy',
+    U: 'Ura'
+  },
+  monophosphate: {
     A: 'Amp',
@@ -84,2 +121,17 @@ C: 'Cmp',
     U: 'Ump'
+  },
+  diphosphate: {
+    A: 'Adp',
+    C: 'Cdp',
+    G: 'Gdp',
+    T: 'Tdp',
+    U: 'Udp'
+  },
+  triphosphate: {
+    A: 'Atp',
+    C: 'Ctp',
+    G: 'Gtp',
+    T: 'Ttp',
+    U: 'Utp'
+  }
 };

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

12597

increased by155.1%

Number of package files

10

increased by100%

Lines of code

302

increased by228.26%

Worsened metrics

Dev dependency count

1

increased byInfinity%

Number of medium supply chain risk alerts

1

increased byInfinity%

No dependency changes