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* The stage's export card (SPECS §27.8): the edit written as the files the
* tools downstream take — the assembly's text files, its sequence, the map and
* the session's tracks lifted through it — and an AGP or a Juicebox
* `.assembly` read back as one.
*
* Every file leaves through the save dialog (§26.6), asked from the press
* itself before anything is made for it, and none of them touches a file the
* session opened. A file read back is one step of the history — *lay out as in*
* it — so it is undone as any step is.
*/
import { sequenceSets } from './dotplotLines'
import { agpOf, chainOf, chromSizesOf, juiceboxAssemblyOf, readAgp, readJuiceboxAssembly, writableEdit, type ExportContext, type ReadBack } from './exports'
import { fastaOf, liftedFeaturesBed, liftedPairsBedpe, liftedSignal, type LiftContext } from './lifted'
import { writeBigWig } from '../analysis/write/bigwig'
import { formatBp } from '../pairs/import'
import type { AnnotationEntry } from '../annotations/types'
import type { AnnotationStore } from '../annotations/store'
import type { AnnotationClient } from '../annotations/worker/client'
import { EditedAssembly, type ReferenceEdit } from '../genome/edit'
import type { EditStore } from '../state/referenceEdit'
import { el } from '../ui/dom'
import { chooseSaveTarget, exportBaseName, type SaveTarget } from '../ui/export'
import { fmt } from '../units'
import { PRODUCER } from '../version'
import type { LiftedExport } from '../worker/protocol'
import type { BinningTable } from './binning'
import { stepText } from './words'
/** The extensions a map's name ends in, taken off before an export's is put on. */
const MAP_EXTENSIONS = /\.(mcool|cool|hic|mmetacool|metacool|scool|pairs\.gz|pairs|pairs\.bgz)$/i
/** A file's stem: its own name, without a path, a group or the map's extension. */
export function exportStem(title: string): string {
const name = title.split('::')[0].split(/[\\/]/).pop() ?? title
return exportBaseName(name.replace(MAP_EXTENSIONS, ''))
}
/** The text files, in the order the card offers them. */
const TEXT_FILES = [
{ label: 'AGP', suffix: 'edited.agp', title: 'The edited assembly as an AGP 2.1: every sequence as the pieces of the original it is built from' },
{ label: 'chrom.sizes', suffix: 'edited.chrom.sizes', title: 'Every sequence of the edited assembly and its length' },
{ label: '.assembly', suffix: 'edited.assembly', title: 'A Juicebox .assembly, for JBAT, 3D-DNA and YaHS' },
{ label: 'chain', suffix: 'to-edited.chain', title: 'A liftOver chain from the original coordinates to the edited ones, for liftOver or CrossMap' },
] as const
type TextFile = (typeof TEXT_FILES)[number]['label']
/** A long export in flight, and the way to stop it. */
export interface LiftJob<T> {
promise: Promise<T>
cancel(): void
}
export interface ExportCardProps {
/** The map's name, which every file is named after. */
title: string
store: EditStore
/** The session's tracks, and the client that reads them: the sequence and the tracks lifted. */
annotations?: { store: AnnotationStore; client?: AnnotationClient }
/** The map lifted through an edit, every rung, by the reader's worker. */
liftContacts?: (edit: ReferenceEdit, onProgress: (done: number, total: number, note?: string) => void) => LiftJob<LiftedExport>
/**
* On a metagenome (§27.10): the contig → MAG table every genome's edit
* makes of the file's contigs, as it stands when asked.
*/
binning?: () => BinningTable
/** When a file is written, for its header; a clock the tests can hold. */
now?: () => Date
}
/** What a track is written as, lifted: by its kind. */
function formatOf(entry: AnnotationEntry): { label: string; suffix: string } | null {
if (entry.status !== 'ready') return null
if (entry.kind === 'track' && entry.derivedFrom === undefined) return { label: 'bigWig', suffix: 'bw' }
if (entry.payload?.kind === 'features') return { label: 'BED', suffix: 'bed' }
if (entry.payload?.kind === 'pairs') return { label: 'BEDPE', suffix: 'bedpe' }
return null
}
export class ExportCard {
readonly element: HTMLElement
private readonly status: HTMLElement
private readonly picker: HTMLInputElement
private readonly trackSelect: HTMLSelectElement
private job: { cancel(): void } | null = null
private cancelled = false
constructor(private readonly props: ExportCardProps) {
this.status = el('p', { class: 'edit-note edit-export-status', attrs: { role: 'status' } })
this.picker = el('input', {
class: 'hidden',
attrs: { type: 'file', accept: '.agp,.assembly,.txt,text/plain' },
on: { change: () => void this.readPicked() },
})
this.trackSelect = el('select', { class: 'select edit-export-track', attrs: { 'aria-label': 'The track to lift' }, on: { change: () => this.paint() } })
this.element = el('section', { class: 'edit-card edit-export-card' })
this.paint()
}
/**
* The session's sequence, where it has one ready: the file's own, as the
* stage's corner plot and its evidence choose it (`sequenceSets`) — not the
* first set loaded, which may be the other reference the plot sets it
* against, and from which the edited sequence came out as `N`.
*/
private sequenceEntry(): AnnotationEntry | null {
const entries = this.props.annotations?.store.entries
return entries === undefined ? null : sequenceSets(entries).own
}
/** The tracks that can be lifted, with what each is written as. */
private liftable(): Array<{ entry: AnnotationEntry; format: { label: string; suffix: string } }> {
const out: Array<{ entry: AnnotationEntry; format: { label: string; suffix: string } }> = []
for (const entry of this.props.annotations?.store.entries ?? []) {
const format = formatOf(entry)
if (format !== null) out.push({ entry, format })
}
return out
}
/** Draw the card again: its buttons and the line under them. */
paint(): void {
const busy = this.job !== null
const button = (label: string, title: string, run: () => void, disabled = false, format = label): HTMLButtonElement =>
el('button', {
class: 'btn edit-export-file',
text: label,
title,
attrs: { type: 'button', 'data-format': format, ...(disabled || busy ? { disabled: '' } : {}) },
on: { click: run },
})
const files = el(
'div',
{ class: 'edit-export-files' },
...TEXT_FILES.map((file) => button(file.label, file.title, () => void this.write(file.label))),
...(this.props.binning === undefined
? []
: [
button(
'contig → MAG',
'Every contig of the metagenome and the genome it is in, every genome’s edit applied: the two columns DAS_Tool, anvi’o and metacooler create take',
() => void this.writeBinning(),
false,
'binning',
),
]),
)
const sequence = this.sequenceEntry()
const data = el(
'div',
{ class: 'edit-export-files' },
button(
'FASTA',
sequence === null
? 'Load the assembly’s FASTA or .2bit into the session to write the edited sequence'
: `The edited sequence from ${sequence.label}: turned pieces reverse-complemented, gaps as N`,
() => void this.writeFasta(),
sequence === null || this.props.annotations?.client === undefined,
),
button(
'contacts (.mcool)',
'The map lifted through the edit, every rung it has: raw counts, bins moved whole',
() => void this.writeContacts(),
this.props.liftContacts === undefined,
'mcool',
),
)
const liftable = this.liftable()
const chosen = this.trackSelect.value
this.trackSelect.replaceChildren(...liftable.map(({ entry }) => el('option', { text: entry.label, attrs: { value: entry.id } })))
if (liftable.some(({ entry }) => entry.id === chosen)) this.trackSelect.value = chosen
const current = liftable.find(({ entry }) => entry.id === this.trackSelect.value) ?? liftable[0]
const tracks =
liftable.length === 0
? null
: el(
'div',
{ class: 'edit-export-files edit-export-tracks' },
this.trackSelect,
button(
current?.format.label ?? 'BED',
'The track lifted through the edit: a signal as bigWig, features as BED, pairs as BEDPE',
() => void this.writeTrack(),
current === undefined,
'track',
),
)
const read = el(
'div',
{ class: 'edit-export-read' },
button('lay out from an AGP or .assembly…', 'Lay the assembly out as a file describes it: one step of the history, undone as any step is', () => this.picker.click(), false, 'read'),
)
const cancel = busy
? el('button', { class: 'btn-link edit-export-cancel', text: 'cancel', attrs: { type: 'button' }, on: { click: () => this.cancel() } })
: null
this.element.replaceChildren(
el('h3', { class: 'edit-card-head', text: 'export' }),
el('p', { class: 'edit-note', text: 'Written from the edit; no file the session opened is touched.' }),
files,
data,
...(tracks === null ? [] : [tracks]),
read,
el('div', { class: 'edit-export-line' }, this.status, ...(cancel === null ? [] : [cancel])),
this.picker,
)
}
/** What every file's header says about where it came from. */
private context(): ExportContext {
const edit = this.props.store.edit
const now = this.props.now?.() ?? new Date()
return {
file: this.props.title,
by: PRODUCER,
created: now.toISOString(),
steps: edit.history.slice(0, edit.cursor).map((entry) => stepText(entry.step)),
}
}
private liftContext(what: string): LiftContext {
const context = this.context()
return { what, file: context.file, by: context.by, created: context.created }
}
private say(text: string): void {
this.status.textContent = text
}
private name(suffix: string): string {
// One genome's files say whose they are (§27.10).
const genome = this.props.store.edit.original.genome
return `${exportStem(this.props.title)}${genome === undefined ? '' : `.${exportBaseName(genome)}`}.${suffix}`
}
/** Write what `make` makes to where the reader chose, saying so; `make` may be long, and is asked after the dialog. */
private async save(target: SaveTarget, what: string, make: () => Promise<Blob | null>): Promise<void> {
this.cancelled = false
this.job = { cancel: () => (this.cancelled = true) }
this.paint()
try {
const blob = await make()
if (blob === null || this.cancelled) {
this.say(`${what}: cancelled.`)
return
}
await target.write(blob)
this.say(`Wrote ${target.name} (${fmt.bytes(blob.size)}).${this.note === '' ? '' : ` ${this.note}`}`)
} catch (err) {
this.say(`Could not write ${target.name}: ${err instanceof Error ? err.message : String(err)}`)
} finally {
this.note = ''
this.job = null
this.paint()
}
}
/** A line the next write adds to what it says. */
private note = ''
private cancel(): void {
this.cancelled = true
this.job?.cancel()
}
private async write(format: TextFile): Promise<void> {
const file = TEXT_FILES.find((candidate) => candidate.label === format)
if (file === undefined) return
const assembly = this.props.store.assembly
// What cannot be written is said before the dialog opens, not after.
let text: string
if (format === '.assembly') {
const written = juiceboxAssemblyOf(assembly)
if (!written.ok) {
this.say(`No .assembly: ${written.why}.`)
return
}
text = written.text
} else if (format === 'AGP') text = agpOf(assembly, this.context())
else if (format === 'chrom.sizes') text = chromSizesOf(assembly)
else text = chainOf(assembly, this.context())
const target = await chooseSaveTarget(this.name(file.suffix), 'text/plain')
if (target === null) return
await this.save(target, format, async () => new Blob([text], { type: 'text/plain' }))
}
/** The contig → MAG table of the whole metagenome, every genome's edit applied (§27.10). */
private async writeBinning(): Promise<void> {
const binning = this.props.binning
if (binning === undefined) return
const table = binning()
const target = await chooseSaveTarget(`${exportStem(this.props.title)}.contig-mag.tsv`, 'text/tab-separated-values')
if (target === null) return
const count = (n: number, one: string, many: string): string => `${n.toLocaleString('en-US')} ${n === 1 ? one : many}`
this.note =
`${count(table.contigs, 'contig', 'contigs')} in ${count(table.genomes, 'genome', 'genomes')}, ${count(table.moved, 'moved', 'moved')} by the edits.` +
(table.notes.length === 0 ? '' : ` ${table.notes.join('; ')}.`)
await this.save(target, 'contig → MAG', async () => new Blob([table.text], { type: 'text/tab-separated-values' }))
}
/** The edited sequence, piece by piece through the annotation worker's ranged reads. */
private async writeFasta(): Promise<void> {
const entry = this.sequenceEntry()
const client = this.props.annotations?.client
if (entry === null || client === undefined) return
const target = await chooseSaveTarget(this.name('edited.fa'), 'text/plain')
if (target === null) return
const assembly = this.props.store.assembly
await this.save(target, 'FASTA', async () => {
const out = await fastaOf(
assembly,
async (sequence, start, end) => {
const got = await client.request<'bases'>({ kind: 'bases', entry: entry.id, regions: [{ contig: sequence, start, end }] })
return got.regions[0]?.bases ?? null
},
{
onProgress: (done, total) => this.say(`Writing the FASTA · ${Math.floor((100 * done) / Math.max(1, total))}%`),
cancelled: () => this.cancelled,
},
)
if (out === null) return null
if (out.missing.length > 0) {
this.note = `${entry.label} has no ${out.missing.slice(0, 3).join(', ')}${out.missing.length > 3 ? ' and others' : ''}: written as N.`
}
return new Blob(out.parts as BlobPart[], { type: 'text/plain' })
})
}
/** The map lifted through the edit, by the reader's worker. */
private async writeContacts(): Promise<void> {
const lift = this.props.liftContacts
if (lift === undefined) return
const target = await chooseSaveTarget(this.name('edited.mcool'), 'application/octet-stream')
if (target === null) return
const edit = writableEdit(this.props.store.edit)
await this.save(target, 'contacts', async () => {
const job = lift(edit, (done, total, note) =>
this.say(`${note === undefined ? 'Lifting the map' : note[0].toUpperCase() + note.slice(1)} · ${Math.floor((100 * done) / Math.max(1, total))}%`),
)
const previous = this.job
this.job = { cancel: () => { previous?.cancel(); job.cancel() } }
const lifted = await job.promise
const rungs = lifted.rungs.map((size) => formatBp(size)).join(', ')
this.note = `${lifted.rungs.length} rung${lifted.rungs.length === 1 ? '' : 's'}, ${rungs}; ${lifted.contacts.toLocaleString('en-US')} contacts at the finest.${
lifted.skipped.length === 0 ? '' : ` Left out: ${lifted.skipped.map((skip) => `${formatBp(skip.rung)} (${skip.why})`).join('; ')}.`
}`
return new Blob([lifted.bytes as BlobPart], { type: 'application/octet-stream' })
})
}
/** The chosen track lifted through the edit, in the format its kind is written in. */
private async writeTrack(): Promise<void> {
const chosen = this.liftable().find(({ entry }) => entry.id === this.trackSelect.value) ?? this.liftable()[0]
const client = this.props.annotations?.client
if (chosen === undefined) return
const { entry, format } = chosen
const target = await chooseSaveTarget(`${exportBaseName(entry.label)}.edited.${format.suffix}`, format.label === 'bigWig' ? 'application/octet-stream' : 'text/plain')
if (target === null) return
const assembly = this.props.store.assembly
await this.save(target, entry.label, async () => {
const payload = entry.payload
if (payload?.kind === 'features') {
const { text, count } = liftedFeaturesBed(payload.data, assembly, this.liftContext(entry.label))
this.note = liftNote(count.dropped, count.split, 'feature')
return new Blob([text], { type: 'text/plain' })
}
if (payload?.kind === 'pairs') {
const { text, count } = liftedPairsBedpe(payload.data, assembly, this.liftContext(entry.label))
this.note = liftNote(count.dropped, 0, 'pair')
return new Blob([text], { type: 'text/plain' })
}
if (client === undefined) return null
const signal = await liftedSignal(
assembly,
async (sequence, start, end) => {
const got = await client.request<'sample'>({ kind: 'sample', entry: entry.id, regions: [{ contig: sequence, start, end }], basesPerPixel: 1, exact: true })
const region = got.regions[0]
return region === undefined ? null : { starts: region.starts, ends: region.ends, values: region.values, summary: region.summary }
},
{
onProgress: (done, total) => this.say(`Lifting ${entry.label} · ${Math.floor((100 * done) / Math.max(1, total))}%`),
cancelled: () => this.cancelled,
},
)
if (signal === null) return null
if (signal.summary) this.note = 'Some of it came from the file’s zoom levels rather than its own resolution.'
return writeBigWig({ contigs: signal.contigs, spans: signal.spans })
})
}
/** The file the reader picked, read back as a step. */
private async readPicked(): Promise<void> {
const file = this.picker.files?.[0]
this.picker.value = ''
if (file === undefined) return
this.readText(await file.text(), file.name)
}
/**
* A file's text, read back as a layout of the original and made a step —
* an AGP or an `.assembly`, told apart by its first line.
*/
readText(text: string, name: string): ReadBack {
const original = this.props.store.edit.original
const first = text.split(/\r?\n/).find((line) => line.trim() !== '' && !line.startsWith('#')) ?? ''
const read = first.startsWith('>') ? readJuiceboxAssembly(text, original, name) : readAgp(text, original, name)
if (!read.ok) {
this.say(`Not read: ${read.why}.`)
return read
}
this.props.store.apply(read.step, 'reader')
const assembly = EditedAssembly.of(this.props.store.edit)
const count = assembly.sequences.length
const aside = assembly.aside.length
const notes = [...read.notes, ...(aside === 0 ? [] : [`${aside} stretch${aside === 1 ? '' : 'es'} set aside`])]
this.say(`Laid out as in ${name}: ${count} sequence${count === 1 ? '' : 's'}${notes.length === 0 ? '' : `; ${notes.join('; ')}`}.`)
return read
}
}
/** What a lift left out, in words, or nothing. */
function liftNote(dropped: number, split: number, noun: string): string {
const parts: string[] = []
if (dropped > 0) parts.push(`${dropped.toLocaleString('en-US')} ${noun}${dropped === 1 ? '' : 's'} lay on what was set aside and ${dropped === 1 ? 'is' : 'are'} not written`)
if (split > 0) parts.push(`${split.toLocaleString('en-US')} ${noun}${split === 1 ? '' : 's'} an edit cut through, written once per piece`)
return parts.length === 0 ? '' : `${parts.join('; ')}.`
}
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