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MCScanAnchorsAdapter

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

{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg19', 'hg38'],
  adapter: {
    type: 'MCScanAnchorsAdapter',
    uri: 'https://example.com/data.anchors',
    bed1: 'https://example.com/query.bed',
    bed2: 'https://example.com/target.bed',
    assemblyNames: ['hg19', 'hg38'],
  },
}

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

Gotcha

The anchors file carries no coordinates: a gene is placed by matching its id against column 4 of a BED, byte for byte. A row naming a gene neither BED has is dropped, so a partial mismatch draws fewer ribbons than the file holds rather than erroring, and only a file where no row resolves fails the track. Ids get mangled by isoform suffixes, by BLAST truncating a FASTA header at the first space, and by jcvi stripping suffixes unless run with --no_strip_names. BED column 1 has to match the assembly's reference sequence names too, and a name the assembly does not have draws nothing at all.

used to load MCScan (jcvi) .anchors files with their two BED files

See the MCScan anchors tutorial, which also covers converting an MCScanX run into these files.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "MCScanAnchorsAdapter", ... }. It also accepts the shorthand keys uri, baseUri, bed1, bed2, chromSizes, csi, htsgetBase, nhUri in place of writing a location slot out. 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.

SlotDescription
mcscanAnchorsLocation
fileLocation = { uri: '/path/to/mcscan.anchors', locationType: 'UriLocation' }		location of the .anchors file from python -m jcvi.compara.catalog ortholog: one line per anchor pair, naming a gene in each genome. The gene names are resolved to coordinates through the two BED files.
bed1Location
fileLocation = { uri: '/path/to/file.bed', locationType: 'UriLocation' }		BED giving coordinates for the gene names in the anchors file's first column, i.e. the query assembly's genes. Written by python -m jcvi.formats.gff bed.
bed2Location
fileLocation = { uri: '/path/to/file.bed', locationType: 'UriLocation' }		BED giving coordinates for the gene names in the anchors file's second column, i.e. the target assembly's genes.
assemblyNames
stringArray = []		[query, target] — the assembly bed1Location describes, then the one bed2Location describes. Getting the order backwards draws every link against the wrong genome rather than erroring.