b73_converter.ts

b73_converter.ts

import fs from 'fs'

const tracks = JSON.parse(fs.readFileSync(process.argv[2], 'utf8')) as {
  tracks: any[]
}

const asm = 'B73'
const assemblyNames = [asm]
const base = 'https://jbrowse.maizegdb.org/B73/'
console.log(
  JSON.stringify(
    {
      assemblies: [
        {
          name: 'B73',
          sequence: {
            type: 'ReferenceSequenceTrack',
            trackId: 'B73-ReferenceSequenceTrack',
            adapter: {
              type: 'IndexedFastaAdapter',
              uri: `${base}/data/B73v5.fasta`,
            },
          },
        },
      ],
      tracks: tracks.tracks
        .map(t => {
          if (t.urlTemplates) {
            return {
              name: t.key,
              trackId: t.label,
              type: 'MultiQuantitativeTrack',
              category: t.category.split('/'),
              assemblyNames,
              adapter: {
                type: 'MultiWiggleAdapter',
                subadapters: t.urlTemplates.map(f => {
                  console.error({ f })
                  return {
                    ...f,
                    type: 'BigWigAdapter',
                    uri: f.url,
                    source: f.name,
                  }
                }),
              },
            }
          } else if (
            t.urlTemplate.endsWith('bw') ||
            t.urlTemplate.endsWith('.bigwig')
          ) {
            return {
              name: t.key,
              trackId: t.label,
              type: 'QuantitativeTrack',
              category: t.category.split('/'),
              assemblyNames,
              adapter: {
                type: 'BigWigAdapter',
                uri: `${base}/${t.urlTemplate}`,
              },
            }
          } else if (t.urlTemplate.endsWith('trackData.json')) {
            return {
              name: t.key,
              trackId: t.label,
              type: 'FeatureTrack',
              category: t.category.split('/'),
              assemblyNames,
              adapter: {
                type: 'NCListAdapter',
                rootUrlTemplate: {
                  uri: `${base}/${t.urlTemplate}`,
                },
              },
            }
          } else if (t.urlTemplate.endsWith('.bb')) {
            return {
              name: t.key,
              trackId: t.label,
              type: 'FeatureTrack',
              category: t.category.split('/'),
              assemblyNames,
              adapter: {
                type: 'BigBedAdapter',
                uri: `${base}/${t.urlTemplate}`,
              },
            }
          } else {
            return undefined
          }
        })
        .filter(f => !!f),
    },
    null,
    2,
  ),
)

full config here https://s3.amazonaws.com/jbrowse.org/demos/maizegdb/B73/config.json

live https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaizegdb%2FB73%2Fconfig.json