blastNRepr/index.js

"use strict";
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());
    });
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.getBlastRepr = void 0;
const child_process_1 = require("child_process");
const async_exec = (prog, args, onData, onErr) => {
    return new Promise((resolve, reject) => {
        const child = (0, child_process_1.spawn)(prog, args, { shell: true });
        child.stdout.on('data', data => onData(data.toString().trim()));
        child.stderr.on('data', data => onErr(data.toString().trim()));
        child.on('error', err => reject(err));
        child.on('exit', code => resolve(code));
    });
};
const diversitySeq = (Seq) => {
    return Seq.split('').reduce((prev, _curr, id, array) => {
        if (id != 0 && array[id] !== array[id - 1]) {
            return prev + (1 / array.length);
        }
        else {
            return prev;
        }
    }, 0);
};
const annotateSeq = (seq, blastDB, maxBlast = 100, minDiversity = 0.1, blastnPath = 'blastn') => __awaiter(void 0, void 0, void 0, function* () {
    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
        try {
            let results = '';
            let sequence = { sequence: seq };
            if (sequence.sequence) {
                if (diversitySeq(sequence.sequence) > minDiversity) {
                    const sequenceStr = '\'>GG\\n' + sequence.sequence + '\'';
                    yield async_exec('echo', [sequenceStr, '|',
                        blastnPath, '-db', blastDB, '-query', '-', '-outfmt', '6', '-max_target_seqs', '100'], (m) => results += m, console.log);
                    if (results !== '') {
                        //https://www.metagenomics.wiki/tools/blast/blastn-output-format-6
                        const keys = [/*'qseqid',*/ 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'];
                        results.split('\n')
                            .map((it, index) => sequence.blastn = [
                            ...(sequence.blastn || []),
                            Object.assign({ index }, it.split('\t')
                                .slice(1)
                                .reduce((a, v, i) => (Object.assign(Object.assign({}, a), { [keys[i]]: isNaN(parseInt(v)) ? v : parseInt(v) })), {}))
                        ].splice(0, maxBlast));
                        if (sequence.blastn.length === 0) {
                            throw 'Blastn results parsing failed';
                        }
                    }
                    else {
                        // console.log('WARNING NO BLASTN RESULT', ['echo', '-e', ,'\'' + sequenceStr + '\'', '|',
                        // blastn, '-db', blastDB, '-query', '-', '-outfmt', '6', '-max_target_seqs', '100'].join(' '))
                        throw 'No blastn hit';
                    }
                }
                else {
                    throw 'Sequence diversity < ' + minDiversity;
                }
            }
            else {
                throw 'No sequence';
            }
            resolve(sequence);
        }
        catch (error) {
            reject(error);
        }
    }));
});
const transpose = (matrix) => matrix.reduce(($, row) => row.map((_, i) => [...($[i] || []), row[i]]), []);
const whichMax = (arr) => arr.flatMap((v, i) => v === Math.max(...arr) ? i : []);
const getBlastRepr = (args) => __awaiter(void 0, void 0, void 0, function* () {
    const { sequence, dbs } = args;
    try {
        let all_blastn = [];
        for (const cdb of dbs) {
            let res = [];
            try {
                res = yield annotateSeq(sequence, cdb);
                if (res.blastn.length > 0)
                    all_blastn = [...all_blastn, ...res.blastn].map((v, i) => { return Object.assign(Object.assign({}, v), { index: i + 1 }); });
            }
            catch (e) { }
        }
        const indiv_match = all_blastn.map((blastn) => {
            const { start, end } = blastn.qstart <= blastn.qend ? { start: blastn.qstart, end: blastn.qend } : { end: blastn.qstart, start: blastn.qend };
            return sequence.split('').map((_, i) => ((i + 1) >= start && (i + 1) <= end) ? '|' : '_').join('');
        });
        const bestRepr = transpose(indiv_match.map((v) => v.split(''))).map((v) => {
            const tmp = v.map((c, i) => {
                if (c === '|') {
                    return all_blastn[i].length;
                }
                else {
                    return 0;
                }
            });
            if (Math.max(...tmp) === 0) {
                return 0;
            }
            else {
                return whichMax(tmp)[0] + 1;
            }
        });
        let bestReprRed = [];
        let n = 0;
        let start = 0;
        bestRepr.reduce((p, c, i) => {
            if (p !== c) {
                const name = p === 0 ? 'unknown' : all_blastn.filter((v) => v.index === p)[0].sseqid + ":" + all_blastn.filter((v) => v.index === p)[0].sstart + '-' + all_blastn.filter((v) => v.index === p)[0].send;
                bestReprRed.push({ name, n, start, end: i });
                start = (i + 1);
                n = 0;
            }
            n++;
            if (i === (bestRepr.length - 1)) {
                const name = c === 0 ? 'unknown' : all_blastn.filter((v) => v.index === c)[0].sseqid + ":" + all_blastn.filter((v) => v.index === c)[0].sstart + '-' + all_blastn.filter((v) => v.index === c)[0].send;
                bestReprRed.push({ name, n, start, end: i + 1 });
            }
            return c;
        });
        const sup = [sequence, ...indiv_match, bestRepr.join('')];
        return { short: bestReprRed.flatMap((ee) => ee.name + "{" + ee.n + "}").join("<>"), all_blastn, sup, bestReprRed };
    }
    catch (error) {
        console.log(error);
        return 1;
    }
});
exports.getBlastRepr = getBlastRepr;
/*(async()=>{
    const sequence = 'ATCTTCACCACGAACTGCTGCTTGCTCGCTTGCTCCTCAGTCCTAGCTTCATCAAACACTGGTTCCTGGAATCCTGTCTGCTGCTGTCTTCCTAGATTCACTGAATCTTCACCACGAACTGCTGCTTGCTCGCTTGCTCCTCAGTCCTAGCTTCATCAA'
    const dbs = ['/home/thomas/NGS/ref/RNA/human_rna.fna']
    console.log(await getBlastRepr({sequence, dbs}));
    
})()*/