uniprotParser/index.js

"use strict";
// https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.xml.gz
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
    return new (P || (P = Promise))(function (resolve, reject) {
        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
        step((generator = generator.apply(thisArg, _arguments || [])).next());
    });
};
var __asyncValues = (this && this.__asyncValues) || function (o) {
    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
    var m = o[Symbol.asyncIterator], i;
    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.getInteractionsFromEntry = exports.getEntryFromGeneName = exports.getEnrty = exports.readOffset = exports.makeIndex = void 0;
const fast_xml_parser_1 = require("fast-xml-parser");
const fs_1 = __importDefault(require("fs"));
const readline_1 = __importDefault(require("readline"));
const line$ = (path) => readline_1.default.createInterface({
    input: fs_1.default.createReadStream(path),
    crlfDelay: Infinity
});
const makeIndex = (filePath, indexPath) => __awaiter(void 0, void 0, void 0, function* () {
    var e_1, _a;
    indexPath = indexPath || filePath + '.jsi';
    let byteAcc = 0;
    const fromSel = new RegExp("^<entry");
    const toSel = new RegExp("^</entry>");
    const valSel = new RegExp('<accession>');
    let tmp = { values: [] };
    try {
        for (var _b = __asyncValues(line$(filePath)), _c; _c = yield _b.next(), !_c.done;) {
            const line = _c.value;
            if (fromSel.test(line))
                tmp['from'] = byteAcc;
            byteAcc += (line.length + 1);
            if (valSel.test(line))
                tmp['values'].push(line.match("<accession>(.*?)</accession>")[1]); // 'uck 
            if (toSel.test(line)) {
                yield fs_1.default.promises.appendFile(indexPath, tmp.values.join(';') + '\t' + tmp.from + '\t' + byteAcc + '\n');
                tmp = { values: [] };
            }
        }
    }
    catch (e_1_1) { e_1 = { error: e_1_1 }; }
    finally {
        try {
            if (_c && !_c.done && (_a = _b.return)) yield _a.call(_b);
        }
        finally { if (e_1) throw e_1.error; }
    }
});
exports.makeIndex = makeIndex;
const readOffset = (path, from, to) => {
    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
        const size = to - from;
        const buffer = Buffer.alloc(size);
        let filehandle;
        try {
            filehandle = yield fs_1.default.promises.open(path, 'r+');
            yield filehandle.read(buffer, 0, buffer.length, from);
        }
        finally {
            if (filehandle) {
                yield filehandle.close();
                resolve(buffer.toString());
            }
        }
    }));
};
exports.readOffset = readOffset;
const getEntryOffset = (dbPath, accession) => __awaiter(void 0, void 0, void 0, function* () {
    var e_2, _d;
    const indexPath = dbPath + '.jsi';
    if (!fs_1.default.existsSync(indexPath))
        yield makeIndex(dbPath);
    const lineSel = new RegExp(accession);
    try {
        for (var _e = __asyncValues(line$(indexPath)), _f; _f = yield _e.next(), !_f.done;) {
            const line = _f.value;
            if (lineSel.test(line))
                return [Number(line.split('\t')[1]), Number(line.split('\t')[2])];
        }
    }
    catch (e_2_1) { e_2 = { error: e_2_1 }; }
    finally {
        try {
            if (_f && !_f.done && (_d = _e.return)) yield _d.call(_e);
        }
        finally { if (e_2) throw e_2.error; }
    }
    return [0, 0];
});
const getEntry = (dbPath, accession) => __awaiter(void 0, void 0, void 0, function* () {
    const parser = new fast_xml_parser_1.XMLParser({
        ignoreAttributes: false,
        alwaysCreateTextNode: false,
        attributeNamePrefix: "",
        textNodeName: "value",
        allowBooleanAttributes: true,
    });
    const offsets = yield getEntryOffset(dbPath, accession);
    return parser.parse(yield readOffset(dbPath, offsets[0], offsets[1]));
});
exports.getEnrty = getEntry;
const getEntryFromGeneName = (idmappingPath, dbPath, geneName) => __awaiter(void 0, void 0, void 0, function* () {
    const accessions = yield getAccessFromGene(idmappingPath, geneName);
    return yield getEntry(dbPath, accessions[0]); // seems to be always the first with entry
});
exports.getEntryFromGeneName = getEntryFromGeneName;
const getAccessFromGene = (idmappingPath, geneName) => __awaiter(void 0, void 0, void 0, function* () {
    var e_3, _g;
    const sel = new RegExp('Gene_Name\t' + geneName);
    let accessions = [];
    try {
        for (var _h = __asyncValues(line$(idmappingPath)), _j; _j = yield _h.next(), !_j.done;) {
            const line = _j.value;
            if (sel.test(line))
                accessions.push(line.split('\t')[0]);
        }
    }
    catch (e_3_1) { e_3 = { error: e_3_1 }; }
    finally {
        try {
            if (_j && !_j.done && (_g = _h.return)) yield _g.call(_h);
        }
        finally { if (e_3) throw e_3.error; }
    }
    return accessions;
});
const getInteractionsFromEntry = (json) => __awaiter(void 0, void 0, void 0, function* () {
    var _k, _l, _m, _o, _p, _q, _r, _s;
    const blaskList = ['DNA', 'PHOSPHOSERINE', 'MOTIFS', 'INFECTION', 'PROTEIN', 'PROTEINS', 'GAMMA-SECRETASE', 'CALCIUM',
        'MICROBIAL', 'VIRUS', 'HEPATITIS', 'HERPES', 'SIMPLEX', 'RELATED', 'AND', 'CLATHRIN', 'WORTMANNIN',
        'NUCLEOSOME', 'undefined', 'INTEGRINS', 'UBIQUITIN', 'MAGNESIUM'];
    const uniprotIDs = Array.isArray(json.entry.accession) ? json.entry.accession : [json.entry.accession];
    // geneName
    const gnTT = Array.isArray(json.entry.gene) ? json.entry.gene[0] : json.entry.gene;
    let geneName = '';
    if (gnTT === null || gnTT === void 0 ? void 0 : gnTT.name) {
        const gnT = Array.isArray(gnTT.name) ? gnTT.name : [gnTT.name];
        geneName = gnT.filter((e) => e.type === 'primary').map((e) => e.value)[0];
    }
    else if ((_l = (_k = json.entry) === null || _k === void 0 ? void 0 : _k.protein) === null || _l === void 0 ? void 0 : _l.recommendedName) {
        geneName = Array.isArray((_o = (_m = json.entry) === null || _m === void 0 ? void 0 : _m.protein) === null || _o === void 0 ? void 0 : _o.recommendedName) ? (_q = (_p = json.entry) === null || _p === void 0 ? void 0 : _p.protein) === null || _q === void 0 ? void 0 : _q.recommendedName[0] : (_s = (_r = json.entry) === null || _r === void 0 ? void 0 : _r.protein) === null || _s === void 0 ? void 0 : _s.recommendedName;
    }
    // Interactants
    const jecT = Array.isArray(json.entry.comment) ? json.entry.comment : [json.entry.comment];
    const interactants = jecT
        .filter((e) => (e === null || e === void 0 ? void 0 : e.type) === 'interaction')
        .flatMap((e) => ({
        type: 'interactant',
        fromProductId: e.interactant[0].id,
        toProductId: e.interactant[1].id,
        to: e.interactant[1].label,
        nExperiments: Number(e.experiments)
    }));
    const regExp = new RegExp('INTERACTION WITH |Interacts with |complex with ', 'i');
    const geneRegExp = new RegExp(/[A-Z]{1}[A-Z|0-9]{2,}$/);
    // uniprot_comment_text_value
    const commentInteractsWith = jecT
        .filter((e) => { var _a; return (_a = e === null || e === void 0 ? void 0 : e.text) === null || _a === void 0 ? void 0 : _a.value; })
        .filter((e) => regExp.test(e.text.value))
        .map((e) => ({
        to: e.text.value
            .split(/\.|;/)
            .flatMap((ee) => ee.replace(/ *\([^)]*\) */g, ' '))
            .filter((ee) => regExp.test(ee))
            .flatMap((ee) => ee.trim().split(regExp))
            .flatMap((ee) => ee.split(/,| and | /))
            .filter((_) => _)
            .filter((ee) => geneRegExp.test(ee))
            .filter((ee) => !blaskList.includes(ee) && ee !== geneName)
            .map((ee) => ee.trim()),
        text: e.text.value,
        //evidences: e.text.evidence.split(' ')//.map((ee:string)=> json.entry.reference.filter((eee:any)=> eee.key === ee)) // Doesnt work with ref key
    }))
        .flatMap((e) => e.to.flatMap((ee) => ({
        type: 'uniprot_comment_text_value',
        to: ee,
        text: e.text
    })));
    // uniprot_reference_scope
    const jerT = Array.isArray(json.entry.reference) ? json.entry.reference : [json.entry.reference];
    const referenceInteract = jerT
        .map((e) => (Object.assign(Object.assign({}, e), { scope: Array.isArray(e.scope) ? e.scope : [e.scope] })))
        .filter((e) => regExp.test(e.scope.join('')))
        .map((e) => (Object.assign({ to: e.scope
            //.split(/\.|;/)
            .flatMap((ee) => regExp.test(ee) ? [ee] : [])
            .filter((_) => _)
            .flatMap((ee) => ee.replace(/ *\([^)]*\) */g, ' '))
            .filter((ee) => regExp.test(ee))
            .flatMap((ee) => ee.trim().split(regExp)[1])
            .flatMap((ee) => ee.split(/,| and | /i))
            .filter((_) => _)
            .filter((ee) => geneRegExp.test(ee))
            .filter((ee) => !blaskList.includes(ee) && ee !== geneName)
            .map((ee) => ee.trim()) }, e)))
        .flatMap((e) => e.to.flatMap((ee) => ({
        type: 'reference_scope',
        to: ee,
        scope: e.scope,
        citation: e.citation
    })));
    // Group
    const byTo = {};
    [...interactants, ...referenceInteract, ...commentInteractsWith]
        .map((e) => byTo[e.to] = byTo[e.to] ? Object.assign(Object.assign({}, e), byTo[e.to]) : Object.assign({}, e));
    const results = Object.keys(byTo).map((e) => {
        var _a;
        (_a = byTo[e]) === null || _a === void 0 ? true : delete _a.to;
        return {
            from: geneName,
            to: e,
            data: byTo[e]
        };
    })
        .filter((e) => !blaskList.includes(e.to) && e.to !== geneName);
    return results;
});
exports.getInteractionsFromEntry = getInteractionsFromEntry;