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Support plaintext fasta on desktop by dynamically creating a FAI file…
… on the fly (#2443)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -16,3 +16,4 @@ yarn-debug.log* | |
| yarn-error.log* | ||
| coverage/ | ||
| public/electron.js | ||
| public/generateFastaIndex.js | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| import fs from 'fs' | ||
| import split2 from 'split2' | ||
| import pump from 'pump' | ||
| import { Readable, Transform } from 'stream' | ||
| import { IncomingMessage } from 'http' | ||
| import { http, https, FollowResponse } from 'follow-redirects' | ||
|
|
||
| export async function createRemoteStream(urlIn: string) { | ||
| const newUrl = new URL(urlIn) | ||
| const fetcher = newUrl.protocol === 'https:' ? https : http | ||
|
|
||
| return new Promise<IncomingMessage & FollowResponse>((resolve, reject) => | ||
| fetcher.get(urlIn, resolve).on('error', reject), | ||
| ) | ||
| } | ||
|
|
||
| export async function getFileStream( | ||
| location: { uri: string } | { localPath: string }, | ||
| ) { | ||
| let fileDataStream: Readable | ||
| // marked as unsed, could be used for progress bar though | ||
| // eslint-disable-next-line @typescript-eslint/no-unused-vars | ||
| let totalBytes = 0 | ||
| // eslint-disable-next-line @typescript-eslint/no-unused-vars | ||
| let receivedBytes = 0 | ||
| let filename: string | ||
|
|
||
| if ('localPath' in location) { | ||
| filename = location.localPath | ||
| totalBytes = fs.statSync(filename).size | ||
| fileDataStream = fs.createReadStream(filename) | ||
| } else if ('uri' in location) { | ||
| filename = location.uri | ||
| const temp = await createRemoteStream(filename) | ||
| totalBytes = +(temp.headers['content-length'] || 0) | ||
| fileDataStream = temp | ||
| } else { | ||
| throw new Error(`Unknown file handle type ${JSON.stringify(location)}`) | ||
| } | ||
|
|
||
| fileDataStream.on('data', chunk => { | ||
| receivedBytes += chunk.length | ||
| }) | ||
| return fileDataStream | ||
| } | ||
|
|
||
| // creates an FAI file from a FASTA file streaming in | ||
| class FastaIndexTransform extends Transform { | ||
| foundAny = false | ||
| possibleBadLine = undefined as [number, string] | undefined | ||
| refName: string | undefined | ||
| currOffset = 0 | ||
| refSeqLen = 0 | ||
| lineBytes = 0 | ||
| lineBases = 0 | ||
| refOffset = 0 | ||
| lineNum = 0 | ||
|
|
||
| _transform(chunk: Buffer, encoding: unknown, done: (error?: Error) => void) { | ||
| const line = chunk.toString() | ||
| // line length in bytes including the \n that we split on | ||
| const currentLineBytes = chunk.length + 1 | ||
| // chop off \r if exists | ||
| const currentLineBases = line.trim().length | ||
| if (line[0] === '>') { | ||
| this.foundAny = true | ||
| if ( | ||
| this.possibleBadLine && | ||
| this.possibleBadLine[0] !== this.lineNum - 1 | ||
| ) { | ||
| done(new Error(this.possibleBadLine[1])) | ||
| return | ||
| } | ||
| if (this.lineNum > 0) { | ||
| this.push( | ||
| `${this.refName}\t${this.refSeqLen}\t${this.refOffset}\t${this.lineBases}\t${this.lineBytes}\n`, | ||
| ) | ||
| } | ||
| // reset | ||
| this.lineBytes = 0 | ||
| this.refSeqLen = 0 | ||
| this.lineBases = 0 | ||
| this.refName = line.trim().slice(1).split(/\s+/)[0] | ||
| this.currOffset += currentLineBytes | ||
| this.refOffset = this.currOffset | ||
| this.possibleBadLine = undefined | ||
| } else { | ||
| if (this.lineBases && currentLineBases !== this.lineBases) { | ||
| this.possibleBadLine = [ | ||
| this.lineNum, | ||
| `Not all lines in file have same width, please check your FASTA file line ${this.lineNum}`, | ||
| ] | ||
| } | ||
| this.lineBytes = currentLineBytes | ||
| this.lineBases = currentLineBases | ||
| this.currOffset += currentLineBytes | ||
| this.refSeqLen += currentLineBases | ||
| } | ||
|
|
||
| this.lineNum++ | ||
| done() | ||
| } | ||
|
|
||
| _flush(done: (error?: Error) => void) { | ||
| if (!this.foundAny) { | ||
| done( | ||
| new Error( | ||
| 'No sequences found in file. Ensure that this is a valid FASTA file', | ||
| ), | ||
| ) | ||
| } else { | ||
| if (this.lineNum > 0) { | ||
| this.push( | ||
| `${this.refName}\t${this.refSeqLen}\t${this.refOffset}\t${this.lineBases}\t${this.lineBytes}\n`, | ||
| ) | ||
| } | ||
| done() | ||
| } | ||
| } | ||
| } | ||
|
|
||
| export async function generateFastaIndex( | ||
| faiPath: string, | ||
| fileDataStream: Readable, | ||
| ) { | ||
| return new Promise((resolve, reject) => { | ||
| pump( | ||
| fileDataStream, | ||
| split2(/\n/), | ||
| new FastaIndexTransform(), | ||
| fs.createWriteStream(faiPath), | ||
| function (err) { | ||
| if (err) { | ||
| reject(err) | ||
| } else { | ||
| resolve('success') | ||
| } | ||
| }, | ||
| ) | ||
| }) | ||
| } |
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