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* The contig → MAG table of a metagenome with every genome's edit applied
* (SPECS §27.10): the binning the edits make, in the two columns DAS_Tool,
* anvi'o and `metacooler create` take — a contig and its genome, one a line,
* no header, a contig of no genome left out.
*
* By the file's own contigs, so it applies to the assembly the reads were
* mapped to: a contig a genome's edit sent to another is that genome's, one a
* genome brought in is its, one set aside as a contaminant with nowhere to go,
* as debris or as a haplotig is no genome's. How a genome's contigs are
* ordered, turned and joined is its AGP's to say, not this table's.
*/
import { EditedAssembly, isGap, type ReferenceEdit } from '../genome/edit'
/** The name the format gives no genome, which the table leaves out. */
export const UNBINNED = '__unbinned__'
/** The table, and what it says about how it was made. */
export interface BinningTable {
text: string
/** Contigs listed, and genomes they are in. */
contigs: number
genomes: number
/** Contigs whose genome an edit changed. */
moved: number
/** What a reader should know: a contig two genomes claim, one only part of which was moved. */
notes: string[]
}
/**
* The binning every genome's edit makes of the file's contigs.
*
* @param contigs Every contig of the file, in its order, with the genome the
* file puts it in.
* @param edits Each genome's edit, where it has one.
*/
export function binningTable(contigs: ReadonlyArray<{ name: string; genome: string }>, edits: ReadonlyMap<string, ReferenceEdit>): BinningTable {
const genomeOf = new Map(contigs.map((contig) => [contig.name, contig.genome]))
const file = new Map(genomeOf)
// Who claims each contig, genome by genome in the file's order of them.
const claimed = new Map<string, string>()
const notes: string[] = []
const order = [...new Set(contigs.map((contig) => contig.genome))].filter((genome) => edits.has(genome))
for (const genome of order) {
const edit = edits.get(genome)
if (edit === undefined || edit.cursor === 0) continue
const assembly = EditedAssembly.of(edit)
const placed = new Set<string>()
for (const sequence of assembly.sequences) for (const part of sequence.parts) if (!isGap(part)) placed.add(part.sequence)
const leaving = new Map<string, string>()
for (const item of assembly.aside) {
const name = item.piece.sequence
if (item.why === 'unplaced') {
placed.add(name)
continue
}
leaving.set(name, item.genome ?? UNBINNED)
}
// What the edit keeps is the genome's; what it sent away, the other's —
// unless some of it stays, which keeps it here and is said.
for (const name of placed) {
const before = claimed.get(name)
if (before !== undefined && before !== genome && file.get(name) !== genome) {
notes.push(`${name} is brought in by both ${before} and ${genome}; the table has it in ${genome}`)
}
claimed.set(name, genome)
}
for (const [name, to] of leaving) {
if (placed.has(name)) {
notes.push(`part of ${name} was sent from ${genome} to ${to === UNBINNED ? 'no genome' : to}, and part kept: the table keeps it in ${genome}`)
continue
}
if (claimed.get(name) === undefined || claimed.get(name) === genome) claimed.set(name, to)
}
// A contig of the genome the edit neither places nor sets aside — a layout
// that left it out, which sets it aside unplaced, is the one way — stays.
}
let moved = 0
const lines: string[] = []
const genomes = new Set<string>()
for (const { name } of contigs) {
const genome = claimed.get(name) ?? genomeOf.get(name) ?? UNBINNED
if (genome !== (file.get(name) ?? UNBINNED)) moved++
if (genome === UNBINNED) continue
lines.push(`${name}\t${genome}`)
genomes.add(genome)
}
return { text: lines.length === 0 ? '' : `${lines.join('\n')}\n`, contigs: lines.length, genomes: genomes.size, moved, notes }
}
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