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nucleotide
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nucleotide - npm Package Compare versions
Comparing version 3.0.3 to 3.1.0
478
lib/index.js
@@ -1,462 +0,20 @@ | ||
| 'use strict'; | ||
| Object.defineProperty(exports, '__esModule', { value: true }); | ||
| var chemicalGroups = require('chemical-groups'); | ||
| var mfUtilities = require('mf-utilities'); | ||
| /** | ||
| * Ensure that the sequence is in uppercase taking into account possible modifications | ||
| * @param {string} [options.circular=false] | ||
| */ | ||
| function ensureUppercaseSequence(sequence) { | ||
| let parenthesisCounter = 0; | ||
| let parts = []; | ||
| let part = ''; | ||
| for (let i = 0; i < sequence.length; i++) { | ||
| let currentSymbol = sequence[i]; | ||
| if (currentSymbol === '(' && parenthesisCounter === 0 && part) { | ||
| parts.push(part); | ||
| part = currentSymbol; | ||
| } else if (currentSymbol === ')' && parenthesisCounter === 0) { | ||
| part += currentSymbol; | ||
| parts.push(part); | ||
| part = ''; | ||
| } else { | ||
| part += currentSymbol; | ||
| "use strict"; | ||
| var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) { | ||
| if (k2 === undefined) k2 = k; | ||
| var desc = Object.getOwnPropertyDescriptor(m, k); | ||
| if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) { | ||
| desc = { enumerable: true, get: function() { return m[k]; } }; | ||
| } | ||
| } | ||
| if (part) parts.push(part); | ||
| for (let i = 0; i < parts.length; i++) { | ||
| if (!parts[i].startsWith('(') && parts[i].match(/^[a-z]+$/)) { | ||
| parts[i] = parts[i].toUpperCase(); | ||
| } | ||
| } | ||
| return parts.join(''); | ||
| } | ||
| /** | ||
| * Convert a nucleic sequence to a MF | ||
| * @param {String} sequence | ||
| * @param {object} [options={}] | ||
| * @param {string} [options.kind] - rna, ds-dna or dna. Default if contains U: rna, otherwise ds-dna | ||
| * @param {string} [options.fivePrime=monophosphate] - alcohol, monophosphate, diphosphate, triphosphate | ||
| * @param {string} [options.circular=false] | ||
| */ | ||
| function sequenceToMF(sequence, options = {}) { | ||
| let fivePrimeTerminal = 'HO'; | ||
| let threePrimeTerminal = 'H'; | ||
| sequence = sequence.replace(/^HO/, ''); | ||
| sequence = sequence.replace(/H$/, ''); | ||
| sequence = sequence.trim(); | ||
| if (sequence === '') return ''; | ||
| sequence = ensureUppercaseSequence(sequence); | ||
| // if the sequence is in lowercase but the parenthesis we should convert it to uppercase | ||
| if (sequence.match(/^[a-z]+$/)) { | ||
| sequence = sequence.toUpperCase(); | ||
| } | ||
| let { kind, circular, fivePrime = 'monophosphate' } = options; | ||
| fivePrime = fivePrime.replace(/[^a-zA-Z]/g, '').toLowerCase(); | ||
| if (!kind) { | ||
| if (sequence.includes('U')) { | ||
| kind = 'rna'; | ||
| } else { | ||
| kind = 'ds-dna'; | ||
| } | ||
| } | ||
| kind = kind.replace(/[^A-Za-z]/g, '').toLowerCase(); | ||
| 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 currentSymbol = sequence[i]; | ||
| while (sequence[i + 1] && sequence[i + 1].match(/[a-z]/)) { | ||
| i++; | ||
| currentSymbol += sequence[i]; | ||
| } | ||
| if (currentSymbol.length > 1) { | ||
| results[0].push(currentSymbol); | ||
| continue; | ||
| } | ||
| 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.replace(/[ \t\r\n]/, ''); | ||
| if (!currentSymbol) continue; | ||
| switch (kind) { | ||
| case 'dna': | ||
| results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]); | ||
| break; | ||
| case 'rna': | ||
| results[0].push(oxyNucleotides[nucleotideType][currentSymbol]); | ||
| break; | ||
| case 'dsdna': | ||
| results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]); | ||
| results[1].unshift( | ||
| desoxyNucleotides[nucleotideType][complementary[currentSymbol]], | ||
| ); | ||
| break; | ||
| default: | ||
| // eslint-disable-next-line no-console | ||
| console.warn(`Nucleotide sequenceToMF: unknown kind: ${kind}`); | ||
| } | ||
| } | ||
| if (!circular) { | ||
| results.forEach((result) => result.unshift(fivePrimeTerminal)); | ||
| results.forEach((result) => result.push(threePrimeTerminal)); | ||
| } | ||
| return results.map((result) => result.join('')).join('.'); | ||
| } | ||
| const complementary = { | ||
| A: 'T', | ||
| T: 'A', | ||
| C: 'G', | ||
| G: 'C', | ||
| Object.defineProperty(o, k2, desc); | ||
| }) : (function(o, m, k, k2) { | ||
| if (k2 === undefined) k2 = k; | ||
| o[k2] = m[k]; | ||
| })); | ||
| var __exportStar = (this && this.__exportStar) || function(m, exports) { | ||
| for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p); | ||
| }; | ||
| const desoxyNucleotides = { | ||
| alcohol: {}, | ||
| monophosphate: {}, | ||
| diphosphate: {}, | ||
| triphosphate: {}, | ||
| }; | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'DNA') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| desoxyNucleotides.alcohol[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'DNAp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'NucleotideP') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'DNApp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| desoxyNucleotides.diphosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'DNAppp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| desoxyNucleotides.triphosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| const oxyNucleotides = { | ||
| alcohol: {}, | ||
| monophosphate: {}, | ||
| diphosphate: {}, | ||
| triphosphate: {}, | ||
| }; | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'RNA') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| oxyNucleotides.alcohol[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'RNAp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| oxyNucleotides.monophosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'NucleotideP') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| oxyNucleotides.monophosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'RNApp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| oxyNucleotides.diphosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| chemicalGroups.groups | ||
| .filter((group) => group.kind === 'RNAppp') | ||
| .forEach((group) => { | ||
| if (group.oneLetter) { | ||
| oxyNucleotides.triphosphate[group.oneLetter] = group.symbol; | ||
| } | ||
| }); | ||
| function furanThreeTerm(nucleotide) { | ||
| // last residue should become a furan | ||
| let parts = nucleotide | ||
| .replace(/ /g, '') | ||
| .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2') | ||
| .split(/ /); | ||
| let last = parts.pop(); | ||
| if (!last.match(/D[atcg]mp(.*)$/)) { | ||
| // eslint-disable-next-line no-console | ||
| console.warn( | ||
| `furanThreeTerm can not remove a non monophosphate nucleic acid: ${last}`, | ||
| ); | ||
| return parts.join('') + last; | ||
| } | ||
| return parts.join('') + last.replace(/D[atcg]mp(.*)$/, 'Furp'); | ||
| } | ||
| function addFiveTerm(mfs, fiveTerm, i, options) { | ||
| if (options.a) mfs.push(`${fiveTerm}O-1H-1$a${i}`); // neutral ok | ||
| if (options.ab && i > 1) mfs.push(`${furanThreeTerm(fiveTerm)}$a${i}-B`); // A minus base | ||
| if (options.b) mfs.push(`${fiveTerm}H$b${i}`); // need to add an hydrogen, see: https://books.google.ch/books?id=B57e37bJjqAC&pg=PA172&lpg=PA172&dq=oligonucleotide+b+fragmentation&source=bl&ots=mRr29Pexx2&sig=1NUQcWV-wuj6o9q81my86AVoRto&hl=fr&sa=X&ved=2ahUKEwjI5M3yn-7fAhUJMewKHQR6Bcs4ChDoATADegQIBhAB#v=onepage&q&f=true | ||
| if (options.c) mfs.push(`${fiveTerm}PO2$c${i}`); // neutral ok | ||
| if (options.d) mfs.push(`${fiveTerm}PO3H2$d${i}`); | ||
| if (options.dh2o) mfs.push(`${fiveTerm}PO2$d${i}-H2O`); | ||
| } | ||
| const mfLosses = {}; | ||
| ['Amp', 'Tmp', 'Cmp', 'Gmp', 'Ump'].forEach((nucleotide) => { | ||
| mfLosses[nucleotide] = { | ||
| code: nucleotide.charAt(0), | ||
| diff: mfUtilities.mfDiff('Rmp', nucleotide), | ||
| }; | ||
| }); | ||
| ['Damp', 'Dtmp', 'Dcmp', 'Dgmp', 'Dump'].forEach((nucleotide) => { | ||
| mfLosses[nucleotide] = { | ||
| code: nucleotide.charAt(1).toUpperCase(), | ||
| diff: mfUtilities.mfDiff('Drmp', nucleotide), | ||
| }; | ||
| }); | ||
| function baseLoss(nucleotide) { | ||
| // any residue can loose a base | ||
| let results = []; | ||
| for (let key in mfLosses) { | ||
| const base = mfLosses[key]; | ||
| if (nucleotide.includes(key)) { | ||
| results.push(`${nucleotide}(${base.diff})$${base.code}*`); | ||
| } | ||
| } | ||
| return results; | ||
| } | ||
| function addFiveTermBaseLoss(mfs, fiveTerm, i, options) { | ||
| if (!options.abcdBaseLoss) return; | ||
| let loss = baseLoss(fiveTerm); | ||
| loss.forEach((mf) => { | ||
| if (options.a) { | ||
| mfs.push(`${mf}`.replace('$', `O-1H-1$a${i} `)); | ||
| } | ||
| if (options.b) { | ||
| mfs.push(`${mf}`.replace('$', `H-1$b${i} `)); | ||
| } | ||
| if (options.c) { | ||
| mfs.push(`${mf}`.replace('$', `PO2$c${i} `)); | ||
| } | ||
| if (options.d) { | ||
| mfs.push(`${mf}`.replace('$', `PO3H2$d${i} `)); | ||
| } | ||
| }); | ||
| } | ||
| // https://books.google.ch/books?id=B57e37bJjqAC&pg=PA172&lpg=PA172&dq=oligonucleotide+b+fragmentation&source=bl&ots=mRr29Pexx2&sig=1NUQcWV-wuj6o9q81my86AVoRto&hl=fr&sa=X&ved=2ahUKEwjI5M3yn-7fAhUJMewKHQR6Bcs4ChDoATADegQIBhAB#v=onepage&q=oligonucleotide%20b%20fragmentation&f=false | ||
| function addInternalTerm(mfs, internal, ter3, ter5, options = {}) { | ||
| if (options.aw) { | ||
| // without base loss | ||
| mfs.push(`HO${internal}O-1H-1$w${ter3}:a${ter5}`); // A W | ||
| } | ||
| if (options.bw) { | ||
| // without base loss | ||
| mfs.push(`HO${internal}H$w${ter3}:b${ter5}`); // B W | ||
| } | ||
| if (options.abw) { | ||
| // with base loss | ||
| let fragment = furanThreeTerm(internal); | ||
| mfs.push(`HO${fragment}$w${ter3}:a${ter5}-B`); // A minus base - W | ||
| } | ||
| if (options.aby) { | ||
| // with base loss | ||
| let fragment = furanThreeTerm(internal); | ||
| mfs.push(`O-2P-1${fragment}$y${ter3}:a${ter5}-B`); // A minus base - Y | ||
| } | ||
| } | ||
| function addThreeTerm(mfs, threeTerm, i, options) { | ||
| if (options.w) mfs.push(`HO${threeTerm}$w${i}`); // neutral ok | ||
| if (options.x) mfs.push(`H-1${threeTerm}$x${i}`); // neutral ok | ||
| if (options.y) mfs.push(`O-2P-1${threeTerm}$y${i}`); // neutral ok | ||
| if (options.z) mfs.push(`O-3H-2P-1${threeTerm}$z${i}`); // neutral ok | ||
| if (options.zch2) mfs.push(`O-3H-4C-1P-1${threeTerm}$z${i}-CH2`); // TODO to confirm | ||
| } | ||
| function addThreeTermBaseLoss(mfs, threeTerm, i, options) { | ||
| if (!options.wxyzBaseLoss) return; | ||
| let loss = baseLoss(threeTerm); | ||
| loss.forEach((mf) => { | ||
| if (options.w) { | ||
| mfs.push(`HO${mf}`.replace('$', `$w${i} `)); | ||
| } | ||
| if (options.x) { | ||
| mfs.push(`H-1${mf}`.replace('$', `$x${i} `)); | ||
| } | ||
| if (options.y) { | ||
| mfs.push(`O-2P-1${mf}`.replace('$', `$y${i} `)); | ||
| } | ||
| if (options.z) { | ||
| mfs.push(`O-3H-1P-1(+)${mf}`.replace('$', `$z${i} `)); | ||
| } | ||
| }); | ||
| } | ||
| function generateFragments(mf, options) { | ||
| if (options === undefined) { | ||
| options = { | ||
| a: false, | ||
| ab: false, | ||
| b: false, | ||
| c: false, | ||
| d: false, | ||
| dh2o: false, | ||
| w: false, | ||
| x: false, | ||
| y: false, | ||
| z: false, | ||
| zch2: false, | ||
| aw: false, | ||
| bw: false, | ||
| abw: false, | ||
| aby: false, | ||
| abcdBaseLoss: false, | ||
| wxyzBaseLoss: false, | ||
| }; | ||
| } | ||
| let mfs = []; | ||
| // need to allow 0-9 to deal with neutral loss | ||
| let mfparts = mf | ||
| .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2') | ||
| .split(/ /); | ||
| let fiveTerm = ''; | ||
| let threeTerm = ''; | ||
| 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++) { | ||
| 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); | ||
| } | ||
| 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); | ||
| } | ||
| } | ||
| } | ||
| return mfs; | ||
| } | ||
| exports.baseLoss = baseLoss; | ||
| exports.furanThreeTerm = furanThreeTerm; | ||
| exports.generateFragments = generateFragments; | ||
| exports.sequenceToMF = sequenceToMF; | ||
| Object.defineProperty(exports, "__esModule", { value: true }); | ||
| __exportStar(require("./sequenceToMF.js"), exports); | ||
| __exportStar(require("./generateFragments.js"), exports); | ||
| __exportStar(require("./furanThreeTerm.js"), exports); | ||
| __exportStar(require("./baseLoss.js"), exports); |
@@ -25,11 +25,11 @@ { | ||
| }, | ||
| "version": "3.0.3", | ||
| "version": "3.1.0", | ||
| "devDependencies": { | ||
| "mf-parser": "^3.1.1" | ||
| "mf-parser": "^3.2.0" | ||
| }, | ||
| "dependencies": { | ||
| "chemical-groups": "^2.1.1", | ||
| "mf-utilities": "^3.1.1" | ||
| "chemical-groups": "^2.2.0", | ||
| "mf-utilities": "^3.2.0" | ||
| }, | ||
| "gitHead": "b9f99ec6f05ce6b0034d35f4ae0452ae653f90c2" | ||
| "gitHead": "28dae91d3b42556a23097ee08acfe4061f276ed0" | ||
| } |
New alerts
Major refactor
Supply chain riskPackage 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
- increased by22.21%
35151
- Number of package files
- increased by143.75%
39
- Lines of code
- increased by15.02%
957
Worsened metrics
- Number of medium supply chain risk alerts
- increased byInfinity%
1
Dependency changes
Updatedchemical-groups@^2.2.0
Updatedmf-utilities@^3.2.0