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chr1
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@cmdcolin
cmdcolin committed Oct 14, 2022
1 parent a9cade4 commit fa1b156
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Showing 3 changed files with 157,799 additions and 78 deletions.
152 changes: 81 additions & 71 deletions src/parse.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,22 @@ const containerAttributes = {
Derives_from: 'derived_features' as const,
}

// this is all a bit more awkward in javascript than it was in perl
function postSet(
obj: Record<string, Record<string, boolean | undefined> | undefined>,
slot1: string,
slot2: string,
) {
let subObj = obj[slot1]
if (!subObj) {
subObj = {}
obj[slot1] = subObj
}
const returnVal = subObj[slot2] || false
subObj[slot2] = true
return returnVal
}

export class FASTAParser {
seqCallback: (sequence: GFF3.GFF3Sequence) => void
currentSequence:
Expand Down Expand Up @@ -44,7 +60,6 @@ interface ParserArgs {
directiveCallback?(directive: GFF3.GFF3Directive): void
sequenceCallback?(sequence: GFF3.GFF3Sequence): void
bufferSize?: number
strictDerives?: boolean
}

interface References {
Expand All @@ -66,7 +81,6 @@ export default class Parser {
// set when the file switches over to FASTA
eof = false
lineNumber = 0
strictDerives = false
// features that we have to keep on hand for now because they
// might be referenced by something else
private _underConstructionTopLevel: GFF3.GFF3Feature[] = []
Expand All @@ -85,6 +99,10 @@ export default class Parser {
// }
// }
private _underConstructionOrphans: Record<string, References | undefined> = {}
private _underConstructionDerivedOrphans: Record<
string,
References | undefined
> = {}

constructor(args: ParserArgs) {
// eslint-disable-next-line @typescript-eslint/no-empty-function
Expand All @@ -96,7 +114,6 @@ export default class Parser {
this.errorCallback = args.errorCallback || nullFunc
this.directiveCallback = args.directiveCallback || nullFunc
this.sequenceCallback = args.sequenceCallback || nullFunc
this.strictDerives = args.strictDerives ?? false

// number of lines to buffer
this.bufferSize = 10000 //args.bufferSize === undefined ? 100000 : args.bufferSize
Expand Down Expand Up @@ -185,8 +202,8 @@ export default class Parser {
item.forEach((i) => {
if (i.child_features)
i.child_features.forEach((c) => _unbufferItem(c))
// if (i.derived_features)
// i.derived_features.forEach((d) => _unbufferItem(d))
if (i.derived_features)
i.derived_features.forEach((d) => _unbufferItem(d))
})
}
}
Expand All @@ -210,6 +227,11 @@ export default class Parser {
private _emitAllUnderConstructionFeatures() {
this._underConstructionTopLevel.forEach(this._emitItem.bind(this))

// output orphan derives from
Object.values(this._underConstructionDerivedOrphans).forEach((f) =>
f?.Derives_from.forEach((f2) => this._emitItem(f2)),
)

this._underConstructionTopLevel = []
this._underConstructionById = {}
this._completedReferences = {}
Expand All @@ -218,13 +240,9 @@ export default class Parser {
// problem. die with a parse error
if (Array.from(Object.values(this._underConstructionOrphans)).length) {
throw new Error(
`some features reference other features that do not exist in the file (or in the same '###' scope). ${JSON.stringify(
this._underConstructionOrphans,
null,
2,
).slice(0, 2000)} ${Object.keys(
`some features reference other features that do not exist in the file (or in the same '###' scope). ${Object.keys(
this._underConstructionOrphans,
)} ll ${JSON.stringify(this._completedReferences, null, 2)}`,
)}. Check if the above IDs exists in file, and if it does exist, increase buffer size and/or add ### lines to file (checkpoints)`,
)
}
}
Expand All @@ -242,9 +260,9 @@ export default class Parser {
// NOTE: a feature is an arrayref of one or more feature lines.
const ids = featureLine.attributes?.ID || []
const parents = featureLine.attributes?.Parent || []
// const derives = featureLine.attributes?.Derives_from || []
const derives = featureLine.attributes?.Derives_from || []

if (!ids.length && !parents.length) {
if (!ids.length && !parents.length && !derives.length) {
// if it has no IDs and does not refer to anything, we can just
// output it
this._emitItem([featureLine])
Expand All @@ -271,7 +289,7 @@ export default class Parser {
feature = [featureLine]

this._enforceBufferSizeLimit(1)
if (!parents.length) {
if (!parents.length && !derives.length) {
this._underConstructionTopLevel.push(feature)
}
this._underConstructionById[id] = feature
Expand All @@ -282,11 +300,8 @@ export default class Parser {
})

// try to resolve all its references
this._resolveReferencesFrom(
feature || [featureLine],
{ Parent: parents, Derives_from: [] },
ids,
)
this._resolveReferencesFrom(feature || [featureLine], parents, ids)
this._resolveReferencesFromDerives(feature || [featureLine], derives, ids)
}

private _resolveReferencesTo(feature: GFF3.GFF3Feature, id: string) {
Expand All @@ -296,14 +311,20 @@ export default class Parser {
// 'Parent' : [ orphans that have a Parent attr referencing this feature ],
// 'Derives_from' : [ orphans that have a Derives_from attr referencing this feature ],
// }
if (!references) return
feature.forEach((loc) => {
loc.child_features.push(...references.Parent)
})
// feature.forEach((loc) => {
// loc.derived_features.push(...references.Derives_from)
// })
delete this._underConstructionOrphans[id]
if (references) {
feature.forEach((loc) => {
loc.child_features.push(...references.Parent)
})
delete this._underConstructionOrphans[id]
}

const references2 = this._underConstructionDerivedOrphans[id]
if (references2) {
feature.forEach((loc) => {
loc.derived_features.push(...references2.Derives_from)
})
delete this._underConstructionDerivedOrphans[id]
}
}

private _parseError(message: string) {
Expand All @@ -313,26 +334,10 @@ export default class Parser {

private _resolveReferencesFrom(
feature: GFF3.GFF3Feature,
references: { Parent: string[]; Derives_from: string[] },
parent: string[],
ids: string[],
) {
// this is all a bit more awkward in javascript than it was in perl
function postSet(
obj: Record<string, Record<string, boolean | undefined> | undefined>,
slot1: string,
slot2: string,
) {
let subObj = obj[slot1]
if (!subObj) {
subObj = {}
obj[slot1] = subObj
}
const returnVal = subObj[slot2] || false
subObj[slot2] = true
return returnVal
}

references.Parent.forEach((toId) => {
parent.forEach((toId) => {
const otherFeature = this._underConstructionById[toId]
if (otherFeature) {
const pname = containerAttributes.Parent
Expand All @@ -357,31 +362,36 @@ export default class Parser {
ref.Parent.push(feature)
}
})

// references.Derives_from.forEach((toId) => {
// const otherFeature = this._underConstructionById[toId]
// if (otherFeature) {
// const pname = containerAttributes.Derives_from
// if (
// !ids.filter((id) =>
// postSet(this._completedReferences, id, `Derives_from,${toId}`),
// ).length
// ) {
// otherFeature.forEach((location) => {
// location[pname].push(feature)
// })
// }
// } else {
// let ref = this._underConstructionOrphans[toId]
// if (!ref) {
// ref = {
// Parent: [],
// Derives_from: [],
// }
// this._underConstructionOrphans[toId] = ref
// }
// ref.Derives_from.push(feature)
// }
// })
}
private _resolveReferencesFromDerives(
feature: GFF3.GFF3Feature,
derives: string[],
ids: string[],
) {
derives.forEach((toId) => {
const otherFeature = this._underConstructionById[toId]
if (otherFeature) {
const pname = containerAttributes.Derives_from
if (
!ids.filter((id) =>
postSet(this._completedReferences, id, `Derives_from,${toId}`),
).length
) {
otherFeature.forEach((location) => {
location[pname].push(feature)
})
}
} else {
let ref = this._underConstructionDerivedOrphans[toId]
if (!ref) {
ref = {
Parent: [],
Derives_from: [],
}
this._underConstructionDerivedOrphans[toId] = ref
}
ref.Derives_from.push(feature)
}
})
}
}
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