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186 changes: 186 additions & 0 deletions
186
packages/core/pluggableElementTypes/models/components/genbank.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,186 @@ | ||
| import { | ||
| AbstractSessionModel, | ||
| Feature, | ||
| max, | ||
| min, | ||
| Region, | ||
| } from '@jbrowse/core/util' | ||
| import { getConf } from '@jbrowse/core/configuration' | ||
|
|
||
| const coreFields = [ | ||
| 'uniqueId', | ||
| 'refName', | ||
| 'source', | ||
| 'type', | ||
| 'start', | ||
| 'end', | ||
| 'strand', | ||
| 'parent', | ||
| 'parentId', | ||
| 'score', | ||
| 'subfeatures', | ||
| 'phase', | ||
| ] | ||
|
|
||
| const blank = ' ' | ||
|
|
||
| const retitle = { | ||
| name: 'Name', | ||
| } as { [key: string]: string | undefined } | ||
|
|
||
| function fmt(obj: unknown): string { | ||
| if (Array.isArray(obj)) { | ||
| return obj.map(o => fmt(o)).join(',') | ||
| } else if (typeof obj === 'object') { | ||
| return JSON.stringify(obj) | ||
| } else { | ||
| return `${obj}` | ||
| } | ||
| } | ||
|
|
||
| function formatTags(f: Feature, parentId?: string, parentType?: string) { | ||
| return [ | ||
| parentId && parentType ? `${blank}/${parentType}="${parentId}"` : '', | ||
| f.get('id') ? `${blank}/name=${f.get('id')}` : '', | ||
| ...f | ||
| .tags() | ||
| .filter(tag => !coreFields.includes(tag)) | ||
| .map(tag => [tag, fmt(f.get(tag))]) | ||
| .filter(tag => !!tag[1] && tag[0] !== parentType) | ||
| .map(tag => `${blank}/${retitle[tag[0]] || tag[0]}="${tag[1]}"`), | ||
| ].filter(f => !!f) | ||
| } | ||
|
|
||
| function rs(f: Feature, min: number) { | ||
| return f.get('start') - min + 1 | ||
| } | ||
| function re(f: Feature, min: number) { | ||
| return f.get('end') - min | ||
| } | ||
| function loc(f: Feature, min: number) { | ||
| return `${rs(f, min)}..${re(f, min)}` | ||
| } | ||
| function formatFeat( | ||
| f: Feature, | ||
| min: number, | ||
| parentType?: string, | ||
| parentId?: string, | ||
| ) { | ||
| const type = `${f.get('type')}`.slice(0, 16) | ||
| const l = loc(f, min) | ||
| const locstrand = f.get('strand') === -1 ? `complement(${l})` : l | ||
| return [ | ||
| ` ${type.padEnd(16)}${locstrand}`, | ||
| ...formatTags(f, parentType, parentId), | ||
| ] | ||
| } | ||
|
|
||
| function formatCDS( | ||
| feats: Feature[], | ||
| parentId: string, | ||
| parentType: string, | ||
| strand: number, | ||
| min: number, | ||
| ) { | ||
| const cds = feats.map(f => loc(f, min)) | ||
| const pre = `join(${cds})` | ||
| const str = strand === -1 ? `complement(${pre})` : pre | ||
| return feats.length | ||
| ? [` ${'CDS'.padEnd(16)}${str}`, `${blank}/${parentType}="${parentId}"`] | ||
| : [] | ||
| } | ||
|
|
||
| export function formatFeatWithSubfeatures( | ||
| feature: Feature, | ||
| min: number, | ||
| parentId?: string, | ||
| parentType?: string, | ||
| ): string { | ||
| const primary = formatFeat(feature, min, parentId, parentType) | ||
| const subfeatures = feature.get('subfeatures') || [] | ||
| const cds = subfeatures.filter(f => f.get('type') === 'CDS') | ||
| const sansCDS = subfeatures.filter( | ||
| f => f.get('type') !== 'CDS' && f.get('type') !== 'exon', | ||
| ) | ||
| const newParentId = feature.get('id') | ||
| const newParentType = feature.get('type') | ||
| const newParentStrand = feature.get('strand') | ||
| return [ | ||
| ...primary, | ||
| ...formatCDS(cds, newParentId, newParentType, newParentStrand, min), | ||
| ...sansCDS | ||
| .map(sub => | ||
| formatFeatWithSubfeatures(sub, min, newParentId, newParentType), | ||
| ) | ||
| .flat(), | ||
| ].join('\n') | ||
| } | ||
|
|
||
| export async function stringifyGenbank({ | ||
| features, | ||
| assemblyName, | ||
| session, | ||
| }: { | ||
| assemblyName: string | ||
| session: AbstractSessionModel | ||
| features: Feature[] | ||
| }) { | ||
| const today = new Date() | ||
| const month = today.toLocaleString('en-US', { month: 'short' }).toUpperCase() | ||
| const day = today.toLocaleString('en-US', { day: 'numeric' }) | ||
| const year = today.toLocaleString('en-US', { year: 'numeric' }) | ||
| const date = `${day}-${month}-${year}` | ||
|
|
||
| const start = min(features.map(f => f.get('start'))) | ||
| const end = max(features.map(f => f.get('end'))) | ||
| const length = end - start | ||
| const refName = features[0].get('refName') | ||
|
|
||
| const l1 = [ | ||
| `${'LOCUS'.padEnd(12)}`, | ||
| `${refName}:${start + 1}..${end}`.padEnd(20), | ||
| ` ${`${length} bp`}`.padEnd(15), | ||
| ` ${'DNA'.padEnd(10)}`, | ||
| `${'linear'.padEnd(10)}`, | ||
| `${'UNK ' + date}`, | ||
| ].join('') | ||
| const l2 = 'FEATURES Location/Qualifiers' | ||
| const seq = await fetchSequence({ | ||
| session, | ||
| assemblyName, | ||
| regions: [{ assemblyName, start, end, refName }], | ||
| }) | ||
| const contig = seq.map(f => f.get('seq') || '').join('') | ||
| const lines = features.map(feat => formatFeatWithSubfeatures(feat, start)) | ||
| const seqlines = ['ORIGIN', `\t1 ${contig}`, '//'] | ||
| return [l1, l2, ...lines, ...seqlines].join('\n') | ||
| } | ||
|
|
||
| async function fetchSequence({ | ||
| session, | ||
| regions, | ||
| signal, | ||
| assemblyName, | ||
| }: { | ||
| assemblyName: string | ||
| session: AbstractSessionModel | ||
| regions: Region[] | ||
| signal?: AbortSignal | ||
| }) { | ||
| const { rpcManager, assemblyManager } = session | ||
| const assembly = assemblyManager.get(assemblyName) | ||
| if (!assembly) { | ||
| throw new Error(`assembly ${assemblyName} not found`) | ||
| } | ||
|
|
||
| const sessionId = 'getSequence' | ||
| return rpcManager.call(sessionId, 'CoreGetFeatures', { | ||
| adapterConfig: getConf(assembly, ['sequence', 'adapter']), | ||
| regions: regions.map(r => ({ | ||
| ...r, | ||
| refName: assembly.getCanonicalRefName(r.refName), | ||
| })), | ||
| sessionId, | ||
| signal, | ||
| }) as Promise<Feature[]> | ||
| } |
80 changes: 80 additions & 0 deletions
80
packages/core/pluggableElementTypes/models/components/gff3.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| import { Feature } from '@jbrowse/core/util' | ||
|
|
||
| const coreFields = [ | ||
| 'uniqueId', | ||
| 'refName', | ||
| 'source', | ||
| 'type', | ||
| 'start', | ||
| 'end', | ||
| 'strand', | ||
| 'parent', | ||
| 'parentId', | ||
| 'score', | ||
| 'subfeatures', | ||
| 'phase', | ||
| ] | ||
|
|
||
| const retitle = { | ||
| id: 'ID', | ||
| name: 'Name', | ||
| alias: 'Alias', | ||
| parent: 'Parent', | ||
| target: 'Target', | ||
| gap: 'Gap', | ||
| derives_from: 'Derives_from', | ||
| note: 'Note', | ||
| description: 'Note', | ||
| dbxref: 'Dbxref', | ||
| ontology_term: 'Ontology_term', | ||
| is_circular: 'Is_circular', | ||
| } as { [key: string]: string } | ||
|
|
||
| function fmt(obj: unknown): string { | ||
| if (Array.isArray(obj)) { | ||
| return obj.map(o => fmt(o)).join(',') | ||
| } else if (typeof obj === 'object') { | ||
| return JSON.stringify(obj) | ||
| } else { | ||
| return `${obj}` | ||
| } | ||
| } | ||
|
|
||
| function formatFeat(f: Feature, parentId?: string, parentRef?: string) { | ||
| return [ | ||
| f.get('refName') || parentRef, | ||
| f.get('source') || '.', | ||
| f.get('type') || '.', | ||
| f.get('start') + 1, | ||
| f.get('end'), | ||
| f.get('score') || '.', | ||
| f.get('strand') || '.', | ||
| f.get('phase') || '.', | ||
| (parentId ? `Parent=${parentId};` : '') + | ||
| f | ||
| .tags() | ||
| .filter(tag => !coreFields.includes(tag)) | ||
| .map(tag => [tag, fmt(f.get(tag))]) | ||
| .filter(tag => !!tag[1]) | ||
| .map(tag => `${retitle[tag[0]] || tag[0]}=${tag[1]}`) | ||
| .join(';'), | ||
| ].join('\t') | ||
| } | ||
| export function formatMultiLevelFeat( | ||
| f: Feature, | ||
| parentId?: string, | ||
| parentRef?: string, | ||
| ): string { | ||
| const fRef = parentRef || f.get('refName') | ||
| const fId = f.get('id') | ||
| const primary = formatFeat(f, parentId, fRef) | ||
| const subs = | ||
| f.get('subfeatures')?.map(sub => formatMultiLevelFeat(sub, fId, fRef)) || [] | ||
| return [primary, ...subs].join('\n') | ||
| } | ||
|
|
||
| export function stringifyGFF3(feats: Feature[]) { | ||
| return ['##gff-version 3', ...feats.map(f => formatMultiLevelFeat(f))].join( | ||
| '\n', | ||
| ) | ||
| } |
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