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MCScanSimpleAnchorsAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the comparative-adapters plugin. View source.

Reads synteny blocks from an MCScan (jcvi) .anchors.simple file and the two BED files that place its genes.

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

Example usage

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

A block row names four genes, the first and last on each side, and the adapter places all four by matching column 4 of a BED byte for byte. A row with any of the four missing is dropped, so a partial mismatch draws fewer blocks than the file holds rather than erroring, and only a file where no row resolves fails the track. Ids get mangled by isoform suffixes 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.

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "MCScanSimpleAnchorsAdapter", ... }. It also accepts the shorthand keys uri, baseUri, bed1, bed2 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
mcscanSimpleAnchorsLocation
fileLocation = 
{ uri: '/path/to/mcscan.anchors.simple', locationType: 'UriLocation' }
location of the .anchors.simple file from python -m jcvi.compara.synteny screen --simple: one line per synteny block, giving only the first and last gene of the block in each genome. That draws whole blocks rather than the per-gene links a full .anchors file gives.
bed1Location
fileLocation = { uri: '/path/to/file.bed', locationType: 'UriLocation' }		BED giving coordinates for the query assembly's gene names — the first two columns of each block line. Written by python -m jcvi.formats.gff bed.
bed2Location
fileLocation = { uri: '/path/to/file.bed', locationType: 'UriLocation' }		BED giving coordinates for the target assembly's gene names — the third and fourth columns of each block line.
assemblyNames
stringArray = []		[query, target] — the assembly bed1Location describes, then the one bed2Location describes. Getting the order backwards draws every block against the wrong genome rather than erroring.