gbffParser/test.js

"use strict";
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
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        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
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var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const fs_1 = __importDefault(require("fs"));
(() => __awaiter(void 0, void 0, void 0, function* () {
    // wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene
    const LRGPath = '/home/thomas/NGS/ref/ncbi/LRG_RefSeqGene';
    // wget https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20211119/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_feature_table.txt.gz
    const tablePath = '/home/thomas/NGS/ref/ncbi/GCF_000001405.39_GRCh38.p13_feature_table.txt';
    // wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/biological_region/human.biological_region.gbff.gz
    const regionDBPath = '/home/thomas/NGS/ref/ncbi/REGIONS/human.biological_region.gbff';
    // wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/refseqgene.[1-7].genomic.gbff.gz
    const geneDBPath = [1, 2, 3, 4, 5, 6, 7].map(n => '/home/thomas/NGS/ref/ncbi/GENES/refseqgene.' + n + '.genomic.gbff');
    // wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.[1-10].rna.gbff.gz
    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 res = await getSymbol('NOTCH1', LRGPath, tablePath, geneDBPath, rnaDBPath)
    // await makeRefSeqFromReg(rnaDBPath, /NM_/, '/home/thomas/NGS/ref/ncbi/RNA/human_NM.fa')
    // await makeRefSeqFromReg(rnaDBPath, /NM_/, 'test/human_NM.fa', 10)
    // const res = await getOffsets(rnaDBPath.map(e => e + '.jsi'), /NR_/)
    //const res = await getData(rnaDBPath, /NM_/, 'test/test-NM.json', '{"name": features[type="gene"].name, "accession": version}')
    //const res = await getData(geneDBPath, /^NG_007458/, 'test/NOCTH1-gene.json')
    // await fs.promises.writeFile('test/NOCTH1-gene.json', JSON.stringify(res, null , 4))
    const txt = yield fs_1.default.promises.readFile('test/NOCTH1-gene.json');
    const json = JSON.parse(txt.toString());
    console.log(json[0].features.filter((f) => f.type !== 'variation'));
    yield fs_1.default.promises.writeFile('test/gene-feat.json', JSON.stringify(json[0].features.filter((f) => f.type !== 'variation'), null, 4));
}))();