nucleotide - npm Package Compare versions

Comparing version 0.5.11 to 0.6.2

package.json

 {
-  "name": "nucleotide",
-  "version": "0.5.11",
-  "description": "Deal with nucleotides and molecular formula",
-  "module": "src/index.js",
-  "files": [
-    "src"
-  ],
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/cheminfo/molecular-formula.git"
-  },
-  "keywords": [],
-  "author": "Luc Patiny",
-  "license": "MIT",
-  "bugs": {
-    "url": "https://github.com/cheminfo/molecular-formula/issues"
-  },
-  "homepage": "https://github.com/cheminfo/molecular-formula/tree/master/packages/nucleotide#readme"
+    "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"
 }

src/__tests__/test.js

@@ -6,5 +6,23 @@ 'use strict';
 describe('test nucleotide', () => {
-    test('sequenceToMF of AAA return ', () => {
-        expect(Nucleotide.sequenceToMF('AAA')).toEqual('HODampDampDampH');
+    test('sequenceToMF of ATC ', () => {
+        expect(Nucleotide.sequenceToMF('ATC')).toEqual(
+            'HOAmpTmpCmpH.HOGmpAmpTmpH'
+        );
     });
+
+    test('sequenceToMF of AAU ', () => {
+        expect(Nucleotide.sequenceToMF('AAU')).toEqual('HOAmpAmpUmpH');
+    });
+
+    test('sequenceToMF of circular AAA ', () => {
+        expect(Nucleotide.sequenceToMF('AAA', { circular: true })).toEqual(
+            'AmpAmpAmp.TmpTmpTmp'
+        );
+    });
+
+    test('sequenceToMF of DNA AAA ', () => {
+        expect(Nucleotide.sequenceToMF('AAA', { kind: 'DNA' })).toEqual(
+            'HODampDampDampH'
+        );
+    });
 });

src/index.js

 'use strict';
 
+/**
+ * Convert a nucleic sequence to a MF
+ * @param {String} sequence
+ * @param {object} [options={}]
+ * @param {string} [options.kind] - rna, ds-dna or dna. Default if contains U: rna, otherwise ds-dna
+ * @param {string} [options.circular=false]
+ */
+
 function sequenceToMF(sequence, options = {}) {
-    let { dna, rna, circular } = options;
+    let { kind, circular } = options;
     sequence = sequence.toUpperCase().replace(/[^ATCGU]/g, '');
-    if (!dna && !rna) {
+    if (!kind) {
         if (sequence.includes('U')) {
-            rna = true;
+            kind = 'rna';
         } else {
-            dna = true;
+            kind = 'ds-dna';
         }
     }
-    var nucleotides;
-    if (dna) {
-        nucleotides = desoxyNucleotides;
-    } else {
-        nucleotides = oxyNucleotides;
+
+    kind = kind.replace(/[^A-Za-z]/g, '').toLowerCase();
+
+    let results = [[]];
+    if (kind === 'dsdna') results.push([]);
+
+    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}`);
     }
 
-    let result = [];
-    if (!circular) result.push('HO');
-    for (let nucleotide of sequence) {
-        result.push(nucleotides[nucleotide]);
+    if (!circular) {
+        results.forEach((result) => result.unshift('HO'));
+        results.forEach((result) => result.push('H'));
     }
-    if (!circular) result.push('H');
-    return result.join('');
+
+    return results.map((result) => result.join('')).join('.');
 }
@@ -33,2 +60,9 @@
 
+const complementary = {
+    A: 'T',
+    T: 'A',
+    C: 'G',
+    G: 'C'
+};
+
 const desoxyNucleotides = {
@@ -35,0 +69,0 @@ A: 'Damp',

No alert changes

Improved metrics

Total package byte prevSize

4938

increased by48.56%

Lines of code

92

increased by87.76%

No dependency changes