# MCScanBlocksAdapter
Auto-generated config schema for the current JBrowse release — see the
[config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the
`comparative-adapters` plugin.
[View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/comparative-adapters/src/MCScanBlocksAdapter/configSchema.ts).
## Example usage
`uri` is the shorthand for the anchor `.blocks` file:
```js
{
type: 'SyntenyTrack',
trackId: 'my_track',
name: 'My track',
assemblyNames: ['grape', 'peach', 'cacao'],
adapter: {
type: 'MCScanBlocksAdapter',
uri: 'grape.blocks',
blockAssemblies: ['grape', 'peach', 'cacao'],
bedLocations: [
{ uri: 'grape.bed' },
{ uri: 'peach.bed' },
{ uri: 'cacao.bed' },
],
assemblyNames: ['grape', 'peach', 'cacao'],
},
}
```
_See the **Config slots** section below for all available configuration fields._
:::caution Gotcha
`blockAssemblies` and `bedLocations` are positional against the table's own
columns, which is not necessarily the order `assemblyNames` lists or the order
the genomes were given to whatever wrote the table. Get it wrong and every gene
is looked up in another genome's BED; the track fails with the column order
named, rather than drawing empty. The table carries no coordinates: a gene is
placed by matching its id against column 4 of its column's BED, byte for byte.
One column whose BED places none of its ids fails the track naming that column,
since the rest still resolve and only the bands touching that genome would have
been empty. BED column 1 has to match the assembly's reference sequence names,
which is the one mismatch that still draws nothing rather than erroring.
:::
Loads a multi-genome MCScan (jcvi) `.blocks` file: a reference-anchored,
tab-delimited table where column 0 is a reference gene and each further column
is that gene's ortholog in another genome (`.` = no ortholog), produced by
`jcvi.compara.synteny mcscan` + `jcvi.formats.base join`.
A `.blocks` file describes N genomes at once, so one track backs every band of a
multi-way view: list all the genomes in `assemblyNames` and the synteny view
tells the adapter which pair each band draws, deriving that pair's gene links
from the two matching columns. When neither column is the reference the link is
transitive (both orthologous to the same reference gene) rather than a direct
alignment. Listing just two assemblies pins the track to that pair.
Somewhere that names no pair, such as the track shown in a plain linear genome
view or the "Linear synteny view" launcher asking what a locus aligns to, gets
every pair the track declares at once, one set of links per other genome. Group
the display by mate assembly to read them as a lane apiece.
A gene pair the table names on several rows draws once. Both ordinary table
shapes repeat one: a reference-anchored table names a transitive pair again
through each reference gene anchoring it, and an orthogroup table expanded a
copy at a time names every pair not touching that duplication once per row.
See the
[ortholog tables tutorial](https://jbrowse.org/jb2-staging/docs/tutorials/multiway_synteny_grape_peach_cacao),
which covers building the table from jcvi, OrthoFinder, reciprocal best hits or
MCScanX, and stacking the genomes in one view.
## Related links
- **Track:** [SyntenyTrack](../syntenytrack)
- **Display:** [DotplotDisplay](../dotplotdisplay)
- **Display:** [LGVSyntenyDisplay](../lgvsyntenydisplay)
- **Display:** [LinearSyntenyDisplay](../linearsyntenydisplay)
- **Display:** [MultiWaySyntenyDisplay](../multiwaysyntenydisplay)
## Config slots
These slots go inside the track's `adapter`:
`"adapter": { "type": "MCScanBlocksAdapter", ... }`. It also accepts the
[shorthand](https://jbrowse.org/jb2-staging/docs/config_guides/file_types#the-uri-shorthand) keys `uri`,
`baseUri` in place of writing a location slot out. Slot types (`fileLocation`,
`frozen`, ...) are explained in the
[config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a base
configuration contributes are listed here too, so this table is the whole
surface.
| Slot | Description |
| --- | --- |
| **mcscanBlocksLocation**
[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = { uri: '/path/to/mcscan.blocks', locationType: 'UriLocation' } | location of the `.blocks` table: column 0 is a reference gene and each further column is that gene's ortholog in another genome, `.` where there is none. `blockAssemblies` names the columns and `bedLocations` resolves each column's gene names to coordinates. |
| **blockAssemblies**
`stringArray` = [] | one assembly name per column of the blocks file, in column order (column 0 is the reference). A genome may hold several columns, which is what `jcvi mcscan` writes above `--iter=1` (a column per chain of synteny blocks, so a duplicated region is a further column of the same genome) and what a self-comparison is; every column of a genome is drawn, so a gene with two copies in its mate draws a link to each |
| **bedLocations**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#frozen) = [] | one BED fileLocation per column of the blocks file, parallel to blockAssemblies, resolving that column's gene ids to coordinates |
| **assemblyNames**
`stringArray` = [] | the assemblies this track can render; list all of blockAssemblies to let one track back every band of a multi-way view (the view picks each band's pair), or just two to pin it to a single pair. Every entry must appear in blockAssemblies. A genome spanning several columns is named once here, not once per column |
| **attributeColumns**
`stringArray` = [] | names for the numeric columns that follow the gene columns, in order, so an ortholog table can carry per-link measurements the format itself has no place for: `["identity", "dn", "ds", "goc_score"]` reads column N as `identity` where N is `blockAssemblies.length`. Each becomes a feature attribute, so it shows in the detail panel, and `dn`/`ds` are what the synteny view's `Color by → dN/dS` reads. A cell of `.`, `NA`, `NULL`, empty or anything non-numeric is a missing value rather than a zero.
These describe the ROW. On a two-genome table a row is one link, which is what makes a per-link measurement meaningful; on an N-genome table a row is an orthogroup spanning several pairs, so only a value that describes the whole group belongs there |