30:[] 2e:{"title":"Portable MAF API","cells":[{"id":0,"value":"html`\n

Portable MAF API

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"html`\n

Results

We'll test the parser first and then will try to apply it to compressed files retrieved from GDC

Parsing

Testing parser by loading MAF test file from https://episphere.github.io/maf/TCGA.PAAD.mutect.fea333b5-78e0-43c8-bf76-4c78dd3fac92.DR-10.0.somatic.maf.txt :

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":6,"value":"test=await maf.load('https://episphere.github.io/maf/TCGA.PAAD.mutect.fea333b5-78e0-43c8-bf76-4c78dd3fac92.DR-10.0.somatic.maf.txt')","pinned":true,"hidden":false,"mode":"ojs"},{"id":43,"value":"html`Hurray 😀 !`","pinned":false,"hidden":false,"mode":"ojs"},{"id":35,"value":"html`\n

Downloading individual files

Let's use Richard's query at observablehq.com/@rmoffitt/webgen#mafFileData. The first hit is TCGA.CHOL.varscan.e3ad739d-6baa-4c42-a6f7-786d069239c1.DR-10.0.somatic.maf.gz which leads to download page portal.gdc.cancer.gov/files/e3ad739d-6baa-4c42-a6f7-786d069239c1, which appears to be downloadable through api.gdc.cancer.gov/data/e3ad739d-6baa-4c42-a6f7-786d069239c1.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":47,"value":"testBlob = await maf.getFile('https://api.gdc.cancer.gov/data/e3ad739d-6baa-4c42-a6f7-786d069239c1')","pinned":false,"hidden":false,"mode":"ojs"},{"id":71,"value":"testDataURL=URL.createObjectURL(testBlob)","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"html`\n

Methods

Testing parsing a MAF file into a json object will use maf.js library. If I got it right, the same library will run in nodejs and we can serve it as an API that ingests compressed MAF files. Working on that now ...

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":4,"value":"maf = require('https://episphere.github.io/maf/maf.js')","pinned":true,"hidden":false,"mode":"ojs"},{"id":74,"value":"downloadUrl = 'api.gdc.cancer.gov/data/e3ad739d-6baa-4c42-a6f7-786d069239c1'","pinned":true,"hidden":false,"mode":"ojs"},{"id":76,"value":"blb = (await fetch(downloadUrl,{\n mode:'no-cors'\n})).blob().then(x=>URL.createObjectURL(x))","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W30","stdlib":"1","titling":"auto"}