uniprotParser/fillInteractDB.ts

import {getInteractionsFromEntry, readOffset} from '.'
import fs from 'fs'
import readline from 'readline'
const { Database, aql } = require("arangojs");
import { XMLParser } from 'fast-xml-parser'

const db = new Database({
    url: "http://localhost:8529",
    databaseName: "test",
    auth: { username: "root", password: "test123" },
  });

const line$ = (path: string) => readline.createInterface({
    input: fs.createReadStream(path),
    crlfDelay: Infinity
})

const parser = new XMLParser({
    ignoreAttributes: false, 
    alwaysCreateTextNode: false, 
    attributeNamePrefix: "",
    textNodeName: "value",
    allowBooleanAttributes: true,
})

;(async()=>{
    const uniprotDB = '/home/thomas/NGS/ref/UNIPROT/uniprot_sprot_human.xml' 
    for await (const line of line$(uniprotDB + '.jsi')) {
        const acc = /;/.test(line) ? line.split(';')[0] : line.split(/\t/)[0]
        const [from, to] = [line.split(/\t/)[1], line.split(/\t/)[2]]
        const tmp = parser.parse(await readOffset(uniprotDB, Number(from), Number(to)))

        if(Object.keys(tmp).length === 0) {
            break
        } else {
            try {
                const inter = await getInteractionsFromEntry(tmp)
            } catch (error) {
                console.log(error)
                console.log(acc)
                console.log(tmp.entry.gene)
                console.log(tmp)
                break
            }
        }
    }
})()