altTranscripts/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());
    });
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.openSam = exports.analysisTranscript = void 0;
const child_process_1 = require("child_process");
const gbffparser_1 = require("gbffparser");
const fs_1 = __importDefault(require("fs"));
const os_1 = __importDefault(require("os"));
const path_1 = __importDefault(require("path"));
const async_exec = (prog, args, onData) => {
    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 => console.log(data.toString().trim()))
        child.on('error', err => reject(err));
        child.on('exit', code => resolve(code));
    });
};
const openSam = (filePaths, restraintTo, count) => __awaiter(void 0, void 0, void 0, function* () {
    let accum = '';
    let jsonLines = [];
    filePaths = Array.isArray(filePaths) ? filePaths : [filePaths];
    for (let filePath of filePaths) {
        let args = ['view'];
        if (filePath.match(/\.sam$/)) {
            if (restraintTo) {
                if (!fs_1.default.existsSync(filePath.split(/\.sam$/)[0] + '.bam')) {
                    const tmpBam = path_1.default.join(os_1.default.tmpdir(), Math.random() + '.bam');
                    yield async_exec('sambamba', ['view', '-S', filePath, '-f', 'bam', '>', tmpBam], () => { });
                    filePath = filePath.split(/\.sam$/)[0] + '.bam';
                    yield async_exec('sambamba', ['sort', tmpBam, '-o', filePath], () => { });
                    yield fs_1.default.promises.unlink(tmpBam);
                }
                else {
                    filePath = filePath.split(/\.sam$/)[0] + '.bam';
                }
            }
            else {
                args.push('-S');
            }
        }
        if (!count) {
            args = [...args, '-f', 'json'];
        }
        else {
            //if(restraintTo) {
            args.push('-c');
            //}
        }
        args.push(filePath);
        if (restraintTo)
            args.push(restraintTo);
        const threads = os_1.default.cpus().length - 2 > 0 ? os_1.default.cpus().length - 2 : 1;
        args.push('-t');
        args.push(String(threads));
        console.log(['sambamba', ...args].join(' '));
        yield async_exec('sambamba', args, (m) => {
            accum += m;
            accum = accum.replace('}{', '}\n{');
            if (accum.match('\n')) {
                accum.split('\n').map((e, i, a) => {
                    if (i !== a.length - 1) {
                        try {
                            jsonLines.push(JSON.parse(e));
                        }
                        catch (error) {
                            console.log(error);
                        }
                    }
                    else {
                        accum = e;
                    }
                });
            }
        });
        if (accum !== '') {
            accum = accum.replace('}{', '}\n{');
            accum.split('\n').map((e, i, a) => {
                try {
                    jsonLines.push(JSON.parse(e));
                }
                catch (error) {
                    console.log(error);
                }
            });
        }
    }
    return jsonLines;
});
exports.openSam = openSam;
const extractReads = (reads, fastqPaths) => {
    fastqPaths = Array.isArray(fastqPaths) ? fastqPaths : [fastqPaths];
};
const analysisTranscript = (accession, properBam, splittersSam, disordantsSam, rnaDBPath) => __awaiter(void 0, void 0, void 0, function* () {
    const accessionWoVersion = accession.split(/\.[0-9]{1,3}/)[0];
    const accJson = yield (0, gbffparser_1.getFromAcc)(accessionWoVersion, rnaDBPath);
    let json = {
        sequence: (accJson === null || accJson === void 0 ? void 0 : accJson.sequence) || '',
        version: accJson === null || accJson === void 0 ? void 0 : accJson.version,
        exons: (accJson === null || accJson === void 0 ? void 0 : accJson.features.filter(entry => entry.type === 'exon').map((exon, i) => ({
            n: i + 1,
            start: exon.start,
            end: exon.end,
            strand: exon.strand,
            sequence: accJson.sequence.substring(exon.start - 1, exon.end),
            counts: {},
        }))) || [],
        counts: {},
        altTranscripts: {}
    };
    json.counts.all = yield openSam(properBam, accession, true);
    json.counts.splitters = yield openSam(splittersSam, accession, true);
    json.counts.discordants = yield openSam(disordantsSam, accession, true);
    for (let index = 0; index < json.exons.length; index++) {
        const exon = json.exons[index];
        json.exons[index].counts.all = yield openSam(properBam, accession + ':' + exon.start + '-' + exon.end, true);
        json.exons[index].counts.splitters = yield openSam(splittersSam, accession + ':' + exon.start + '-' + exon.end, true);
        json.exons[index].counts.discordants = yield openSam(disordantsSam, accession + ':' + exon.start + '-' + exon.end, true);
    }
    if (typeof json.exons !== 'undefined') {
        const samJSON = yield openSam([
            'test/bwa_mem_splitters_on_human_NM.sam',
            'test/bwa_mem_discordants_on_human_NM.sam'
        ], accession);
        const byRead = {};
        samJSON.map((entry) => ({
            qname: entry.qname.split('_')[0],
            pos: entry.pos,
            exon: json.exons.flatMap((exon, i) => (exon.start <= entry.pos && exon.end >= entry.pos) ? i + 1 : [])[0]
        }))
            .map((entry) => {
            if (typeof byRead[entry.qname] === 'undefined')
                byRead[entry.qname] = [];
            byRead[entry.qname] = [...new Set([...byRead[entry.qname], entry.exon])].sort((a, b) => a - b);
        });
        const byAltern = {};
        Object.keys(byRead).map(qname => {
            const bridges = byRead[qname].flatMap((e, i) => byRead[qname]
                .flatMap((ee, ii) => i === ii || i >= ii ? [] : e + '-' + ee));
            for (const bridge of bridges) {
                if (typeof byAltern[bridge] === 'undefined')
                    byAltern[bridge] = [];
                byAltern[bridge].push(qname);
            }
        });
        json.altTranscripts = Object.keys(byAltern)
            .map(bridge => ({ bridge, reads: byAltern[bridge] }))
            .sort((a, b) => b.reads.length - a.reads.length);
    }
    return json;
});
exports.analysisTranscript = analysisTranscript;
/*(async()=>{
    // await asyncBwaMem('/home/thomas/NGS/ref/ncbi/RNA/human_NM.fa',
    // ['/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R1.fq.gz','/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R2.fq.gz'],
    // 'TEST', 'TEST', 'test/', console.log)
    
    const symbol = 'NOTCH1'

    const LRGPath = '/home/thomas/NGS/ref/ncbi/LRG_RefSeqGene'
    const tablePath = '/home/thomas/NGS/ref/ncbi/GCF_000001405.39_GRCh38.p13_feature_table.txt'

    const rnaDBPath  = [1,2,3,4,5,6,7,8,9,10].map(n => '/home/thomas/NGS/ref/ncbi/RNA/human.' + n + '.rna.gbff')
    const geneDBPath = [1,2,3,4,5,6,7].map(n => '/home/thomas/NGS/ref/ncbi/GENES/refseqgene.' + n + '.genomic.gbff')
    
    const geneInfo = await getSymbol(symbol, LRGPath, tablePath, geneDBPath, rnaDBPath)
    await fs.promises.writeFile('test/geneInfo.json', JSON.stringify(geneInfo.filter((entry:any) => entry.feature === 'mRNA'), null, 4))
    const transcripts = geneInfo.filter((entry:any) => entry.feature === 'mRNA')
    .map((entry:any) => ({...entry, sequence: entry.data.sequence, data:entry.data.features.filter((feature:any) => feature.type === 'exon')}))
    .map((entry:any) => ({
        accession: entry.product_accession,
        genomic_accession: entry.genomic_accession,
        start: entry.start,
        end: entry.end,
        sequence: entry.sequence,
        exons: [...entry.data.map((d:any) => ({start: d.start, end: d.end}))]
    }))
    .map((entry:any) => ({...entry, exons: entry.exons.map((exon:any) => ({...exon, sequence: entry.sequence.substring(exon.start-1,exon.end)}))}))
    await fs.promises.writeFile('test/sub.json', JSON.stringify(transcripts, null, 4))
    
    for (let index = 0; index < transcripts.length; index++) {
        const transcript = transcripts[index]
        
        transcripts[index].count = {
            all        : await openSam('test/bwa_mem_properly_on_human_NM.sorted.bam', transcript.accession, true),
            splitters  : await openSam('test/bwa_mem_splitters_on_human_NM.sam', transcript.accession, true),
            discordants: await openSam('test/bwa_mem_discordants_on_human_NM.sam', transcript.accession, true),
        }

        const samJSON = await openSam([
            'test/bwa_mem_splitters_on_human_NM.sam',
            'test/bwa_mem_discordants_on_human_NM.sam'],
            transcript.accession)

        const byRead = {} as {[key:string]: number[]}
        samJSON.map((entry:any) => ({
            qname: entry.qname.split('_')[0],
            pos: entry.pos,
            exon: transcript.exons.flatMap((exon:any, i:any) => (exon.start <= entry.pos && exon.end >= entry.pos) ? i + 1 : [])[0]
        }))
        .map((entry:any) => {
            if(typeof byRead[entry.qname] === 'undefined') byRead[entry.qname] = []
            byRead[entry.qname] = [...new Set([...byRead[entry.qname], entry.exon])].sort((a,b) => a - b)
        })

        const byAltern = {} as {[key:string]: string[]}
        Object.keys(byRead).map(qname => {
            const bridges = byRead[qname].flatMap((e,i) => byRead[qname]
            .flatMap((ee,ii) => i === ii || i >= ii ? []: e + '-' + ee))
            for (const bridge of bridges) {
                if(typeof byAltern[bridge] === 'undefined') byAltern[bridge] = []
                byAltern[bridge].push(qname)
            }
        })

        transcripts[index].altTranscripts = Object.keys(byAltern)
        .map(bridge => ({bridge, reads: byAltern[bridge]}))
        .sort((a,b) => b.reads.length - a.reads.length)

        await fs.promises.writeFile('test/altTranscripts-' + transcript.accession + '.json', JSON.stringify(transcripts[index], null, 4))
    }
})()
*/