Convert JBrowse 1 NCList on disk to GFF

convert_jbrowse_nclist_to_gff.ts

import { LocalFile } from 'generic-filehandle'
import NCList from '@gmod/nclist'
const filter = new Set([
  'Start',
  'End',
  'Strand',
  'Source',
  'Seq_id',
  'Name',
  'Score',
  'Id',
  'Type',
  'Subfeatures',
  'Parent',
])
;(async () => {
  const store = new NCList({
    baseUrl: '',
    urlTemplate: process.argv[2] + '/{refseq}/trackData.json',
    readFile: (url: string) => new LocalFile(url).readFile(),
  })

  for await (const feature of store.getFeatures({
    refName: process.argv[3],
    start: 0,
    end: 50_000_000,
  })) {
    const parent = feature.get('parent')
    const name = feature.get('name')
    const rest = feature
      .tags()
      .filter((f: string) => !filter.has(f)) as string[]
    if (rest.length !== 0) {
      console.error(rest.length, rest)
    }
    console.log(
      [
        feature.get('seq_id'),
        feature.get('source'),
        feature.get('type'),
        feature.get('start'),
        feature.get('end'),
        feature.get('score') || '.',
        feature.get('strand') === -1 ? '-' : feature === 1 ? '+' : '.',
        feature.get('phase') || '.',
        [
          `ID=${feature.get('ID')}`,
          parent ? `Parent=${parent}` : '',
          name ? `Name=${name}` : '',
          ...rest.map(r => `${r}=${feature.get(r)}`),
        ]
          .filter(f => !!f)
          .join(';'),
      ].join('\t'),
    )
  }
})()

usage

run it in the data directories "tracks" folder

for j in * ; do touch "$j.gff"; for i in $j/*; do echo $j `basename $i`; node dist/index.js "$j" `basename $i` >> "$j.gff"; done;  done;