nucleotide - npm Package Compare versions

Comparing version 0.12.0 to 0.12.1

package.json

@@ -23,7 +23,7 @@ {
   },
-  "version": "0.12.0",
+  "version": "0.12.1",
   "devDependencies": {
     "mf-parser": "^0.12.0"
   },
-  "gitHead": "aa2e6571c5f7121dda616b7d6920b7a653a8f9c7"
+  "gitHead": "cc0873275c6a22fafb6babe866e8164ee25e0d30"
 }

src/__tests__/addThreeTermBaseLoss.test.js

@@ -9,3 +9,3 @@ 'use strict';
       x: true,
-      wxyzBaseLoss: true
+      wxyzBaseLoss: true,
     });
@@ -17,5 +17,5 @@ expect(fragments).toStrictEqual([
       'H-1DrmpDcmpH$x2-B1',
-      'H-1DtmpDrmpH$x2-B2'
+      'H-1DtmpDrmpH$x2-B2',
     ]);
   });
 });

src/__tests__/generateFragments.internal.test.js

@@ -8,8 +8,8 @@ 'use strict';
     let fragments = generateFragments('HODampDtmpDcmpDgmpDampH', {
-      abw: true
+      abw: true,
     });
     expect(fragments).toStrictEqual([
-      'HODtmpC5H6O4P$w4:a-B3',
-      'HODtmpDcmpC5H6O4P$w4:a-B4',
-      'HODcmpC5H6O4P$w3:a-B4'
+      'HODtmpC5H6O4P$w4:a3-B',
+      'HODtmpDcmpC5H6O4P$w4:a4-B',
+      'HODcmpC5H6O4P$w3:a4-B',
     ]);
@@ -20,11 +20,11 @@ });
     let fragments = generateFragments('HODthyDcmpDcmpDgmpDtmpDcmpH', {
-      aby: true
+      aby: true,
     });
     expect(fragments).toStrictEqual([
-      'O-2P-1DcmpC5H6O4P$y5:a-B3',
-      'O-2P-1DcmpDcmpC5H6O4P$y5:a-B4',
-      'O-2P-1DcmpDcmpDgmpC5H6O4P$y5:a-B5',
-      'O-2P-1DcmpC5H6O4P$y4:a-B4',
-      'O-2P-1DcmpDgmpC5H6O4P$y4:a-B5',
-      'O-2P-1DgmpC5H6O4P$y3:a-B5'
+      'O-2P-1DcmpC5H6O4P$y5:a3-B',
+      'O-2P-1DcmpDcmpC5H6O4P$y5:a4-B',
+      'O-2P-1DcmpDcmpDgmpC5H6O4P$y5:a5-B',
+      'O-2P-1DcmpC5H6O4P$y4:a4-B',
+      'O-2P-1DcmpDgmpC5H6O4P$y4:a5-B',
+      'O-2P-1DgmpC5H6O4P$y3:a5-B',
     ]);
@@ -37,4 +37,4 @@ });
       {
-        abw: true
-      }
+        abw: true,
+      },
     );
@@ -46,3 +46,3 @@ expect(fragments).toMatchSnapshot();
     let fragments = generateFragments('HODampDtmpDcmpDgmpDampH', {
-      aw: true
+      aw: true,
     });
@@ -52,3 +52,3 @@ expect(fragments).toStrictEqual([
       'HODtmpDcmpDgmpO-1H-1$w4:a4',
-      'HODcmpDgmpO-1H-1$w3:a4'
+      'HODcmpDgmpO-1H-1$w3:a4',
     ]);
@@ -59,3 +59,3 @@ });
     let fragments = generateFragments('HODampDtmpDcmpDgmpDampH', {
-      bw: true
+      bw: true,
     });
@@ -65,3 +65,3 @@ expect(fragments).toStrictEqual([
       'HODtmpDcmpDgmpH$w4:b4',
-      'HODcmpDgmpH$w3:b4'
+      'HODcmpDgmpH$w3:b4',
     ]);
@@ -72,6 +72,6 @@ });
     let fragments = generateFragments('HODampDampDtmp(NH2)DampH', {
-      abw: true
+      abw: true,
     });
-    expect(fragments).toStrictEqual(['HODampC5H6O4P$w3:a-B3']);
+    expect(fragments).toStrictEqual(['HODampC5H6O4P$w3:a3-B']);
   });
 });

src/__tests__/generateFragments.test.js

@@ -11,2 +11,28 @@ 'use strict';
 
+  it('nucleotide to sequence of HODampDtmp(H-1(Cl)Na)DcmpH', () => {
+    let fragments = generateFragments('HODampDtmp(H-1(Cl)Na)DcmpH', {
+      a: true,
+      z: true,
+    });
+    expect(fragments).toStrictEqual([
+      'HODampO-1H-1$a1',
+      'O-3H-2P-1DcmpH$z1',
+      'HODampDtmp(H-1(Cl)Na)O-1H-1$a2',
+      'O-3H-2P-1Dtmp(H-1(Cl)Na)DcmpH$z2',
+    ]);
+  });
+
+  it('nucleotide to sequence of (HO)DampDtmpDcmp(H)', () => {
+    let fragments = generateFragments('(HO)DampDtmpDcmp(H)', {
+      a: true,
+      z: true,
+    });
+    expect(fragments).toStrictEqual([
+      '(HO)DampO-1H-1$a1',
+      'O-3H-2P-1Dcmp(H)$z1',
+      '(HO)DampDtmpO-1H-1$a2',
+      'O-3H-2P-1DtmpDcmp(H)$z2',
+    ]);
+  });
+
   it('nucleotide to sequence internal modification of HODamp(NH2)DtmpDcmpH', () => {
@@ -13,0 +39,0 @@ let fragments = generateFragments('HODamp(NH2)DtmpDcmpH', { a: true });

src/__tests__/nucleotide.test.js

@@ -43,3 +43,3 @@ 'use strict';
 
-  it('nucleotide to sequence of AAU ', () => {
+  it('nucleotide to sequence of AAU', () => {
     let sequence = Nucleotide.sequenceToMF('AAU');
@@ -51,3 +51,3 @@ expect(sequence).toStrictEqual('HOAmpAmpUmpH');
 
-  it('nucleotide to sequence of circular AAA ', () => {
+  it('nucleotide to sequence of circular AAA', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { circular: true });
@@ -59,3 +59,3 @@ expect(sequence).toStrictEqual('DampDampDamp.DtmpDtmpDtmp');
 
-  it('nucleotide to sequence of DNA AAA ', () => {
+  it('nucleotide to sequence of DNA AAA', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { kind: 'DNA' });
@@ -67,3 +67,3 @@ expect(sequence).toStrictEqual('HODampDampDampH');
 
-  it('nucleotide to sequence of ds-DNA AAA ', () => {
+  it('nucleotide to sequence of ds-DNA AAA', () => {
     let sequence = Nucleotide.sequenceToMF('AAA', { kind: 'ds-DNA' });
@@ -70,0 +70,0 @@ expect(sequence).toStrictEqual('HODampDampDampH.HODtmpDtmpDtmpH');

src/addInternalTerm.js

@@ -21,3 +21,3 @@ 'use strict';
     let fragment = furanThreeTerm(internal);
-    mfs.push(`HO${fragment}$w${ter3}:a-B${ter5}`); // A minus base - W
+    mfs.push(`HO${fragment}$w${ter3}:a${ter5}-B`); // A minus base - W
   }
@@ -28,3 +28,3 @@
     let fragment = furanThreeTerm(internal);
-    mfs.push(`O-2P-1${fragment}$y${ter3}:a-B${ter5}`); // A minus base - Y
+    mfs.push(`O-2P-1${fragment}$y${ter3}:a${ter5}-B`); // A minus base - Y
   }
@@ -31,0 +31,0 @@ }

src/addThreeTerm.js

@@ -8,5 +8,5 @@ 'use strict';
   if (options.z) mfs.push(`O-3H-2P-1${threeTerm}$z${i}`); // neutral ok
-  if (options.zch2) mfs.push(`O-3H-4C-1P-1${threeTerm}$z-CH2${i}`); // TODO to confirm
+  if (options.zch2) mfs.push(`O-3H-4C-1P-1${threeTerm}$z${i}-CH2`); // TODO to confirm
 }
 
 module.exports = addThreeTerm;

src/furanThreeTerm.js

@@ -13,3 +13,3 @@ 'use strict';
     console.warn(
-      `furanThreeTerm can not remove a non monophosphate nucleic acid: ${last}`
+      `furanThreeTerm can not remove a non monophosphate nucleic acid: ${last}`,
     );
@@ -16,0 +16,0 @@ return parts.join('') + last;

src/generateFragments.js

@@ -28,3 +28,3 @@ 'use strict';
       abcdBaseLoss: false,
-      wxyzBaseLoss: false
+      wxyzBaseLoss: false,
     };
@@ -42,2 +42,15 @@ }
 
+  if (mfparts[0].startsWith('(')) {
+    fiveTerm += mfparts[0];
+    mfparts = mfparts.splice(1);
+  }
+
+  if (mfparts[mfparts.length - 1].includes('(')) {
+    threeTerm += mfparts[mfparts.length - 1].replace(/^[^()]*/, '');
+    mfparts[mfparts.length - 1] = mfparts[mfparts.length - 1].replace(
+      /\(.*/,
+      '',
+    );
+  }
+
   for (let ter5 = 1; ter5 < mfparts.length; ter5++) {
@@ -44,0 +57,0 @@ fiveTerm += mfparts[ter5 - 1];

src/index.js

@@ -33,3 +33,3 @@ 'use strict';
     throw new Error(
-      'Nucleotide sequenceToMF: modifications not allowed for ds-DNA'
+      'Nucleotide sequenceToMF: modifications not allowed for ds-DNA',
     );
@@ -67,3 +67,3 @@ }
           console.warn(
-            `Nucleotide sequenceToMF with modification: unknown kind: ${kind}`
+            `Nucleotide sequenceToMF with modification: unknown kind: ${kind}`,
           );
@@ -89,3 +89,3 @@ }
         results[1].unshift(
-          desoxyNucleotides[nucleotideType][complementary[currentSymbol]]
+          desoxyNucleotides[nucleotideType][complementary[currentSymbol]],
         );
@@ -111,3 +111,3 @@ break;
   furanThreeTerm: require('./furanThreeTerm'),
-  baseLoss: require('./baseLoss')
+  baseLoss: require('./baseLoss'),
 };
@@ -119,3 +119,3 @@
   C: 'G',
-  G: 'C'
+  G: 'C',
 };
@@ -129,3 +129,3 @@
     T: 'Dthy',
-    U: 'Dura'
+    U: 'Dura',
   },
@@ -137,3 +137,3 @@ monophosphate: {
     T: 'Dtmp',
-    U: 'Dump'
+    U: 'Dump',
   },
@@ -145,3 +145,3 @@ diphosphate: {
     T: 'Dtdp',
-    U: 'Dudp'
+    U: 'Dudp',
   },
@@ -153,4 +153,4 @@ triphosphate: {
     T: 'Dttp',
-    U: 'Dutp'
-  }
+    U: 'Dutp',
+  },
 };
@@ -164,3 +164,3 @@
     T: 'Thy',
-    U: 'Ura'
+    U: 'Ura',
   },
@@ -172,3 +172,3 @@ monophosphate: {
     T: 'Tmp',
-    U: 'Ump'
+    U: 'Ump',
   },
@@ -180,3 +180,3 @@ diphosphate: {
     T: 'Tdp',
-    U: 'Udp'
+    U: 'Udp',
   },
@@ -188,4 +188,4 @@ triphosphate: {
     T: 'Ttp',
-    U: 'Utp'
-  }
+    U: 'Utp',
+  },
 };

Fixed 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

26571

increased by4.13%

Lines of code

687

increased by5.37%

Number of medium supply chain risk alerts

0

decreased by-100%

No dependency changes