gbffParser/test.ts

import { getSymbol } from '.'

( async () => {
    // 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')

    await getSymbol('NOTCH1', LRGPath, tablePath, geneDBPath, rnaDBPath)
})()