BlastTabularAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the comparative-adapters plugin. View source.

Example usage#

The default columns are BLAST's own -outfmt 6 order, so a file produced without custom columns needs only the two assemblies naming which side is which:

{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['grape', 'peach'],
  adapter: {
    type: 'BlastTabularAdapter',
    blastTableLocation: { uri: 'https://example.com/hits.tsv' },
    assemblyNames: ['grape', 'peach'],
    queryAssembly: 'grape',
    targetAssembly: 'peach',
  },
}

Example: custom outfmt#

If you passed your own column list to -outfmt, repeat it here exactly. qseqid sseqid qstart qend sstart send must be among them; the rest are read where present:

{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['grape', 'peach'],
  adapter: {
    type: 'BlastTabularAdapter',
    blastTableLocation: { uri: 'https://example.com/hits.tsv' },
    assemblyNames: ['grape', 'peach'],
    columns: 'qseqid sseqid qstart qend sstart send evalue',
  },
}

See the Config slots section below for all available configuration fields.

Related links#

• Track: SyntenyTrack
• Display: DotplotDisplay
• Display: LGVSyntenyDisplay
• Display: LinearSyntenyDisplay
• Display: MultiWaySyntenyDisplay
• Guide: Supported file types
• Guide: Synteny track

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "BlastTabularAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'