altTranscripts/test.ts

import fs from 'fs'
import { analysisTranscript, openSam } from '.'

(async()=>{
    const baseDir = '/home/thomas/Turbine-B/Data_2/RNAseqBWA/'
    const rnaDBPath  = [...Array(10).keys()].map(n => '/home/thomas/NGS/ref/ncbi/RNA/human.' + (n+1) + '.rna.gbff')
    const geneDBPath = [...Array(7).keys()].map(n => '/home/thomas/NGS/ref/ncbi/GENES/refseqgene.' + (n+1) + '.genomic.gbff')

    const dirs = fs.readdirSync(baseDir)
    /*const allResults = []
    for (const dir of dirs) {
        console.log(dir)
        const caseDir = baseDir + dir + '/'
        const proper = caseDir + 'bwa_mem_properly_on_human_NM.sorted.bam'
        const splitters = caseDir + 'bwa_mem_splitters_on_human_NM.sam'
        const discordants = caseDir + 'bwa_mem_discordants_on_human_NM.sam'

        const res = await analysisTranscript('NM_017617.5', proper, splitters, discordants, rnaDBPath)
        allResults.push({dir,res})
    }
    await fs.promises.writeFile('test/frommAcc.json', JSON.stringify(allResults, null, 4))*/

    const allCounts = []

    for (const dir of dirs) {
        const r = await openSam(baseDir + dir + '/' + 'bwa_mem_properly_on_human_NM.sorted.bam', '' , true)
        allCounts.push([dir, ...r].join('\t'))
        console.log(allCounts);
        
    }
    console.log(allCounts);
    
    await fs.promises.writeFile('test/allCounts.tsv', allCounts.join('\n'))
    /*const res = JSON.parse((await fs.promises.readFile('test/frommAcc.json')).toString())
    const lines = []

    console.log(res[0].dir);
    
    const txt = res.map((entry:any) => ([entry.dir,...entry.res.exons.reduce((p:any,c:any) => [...p, c.counts.all[0]],[])].join('\t'))).join('\n')
    
    await fs.promises.writeFile('test/CountsByExon.tsv', txt)*/
})()