Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
17
gravatar for martinguerrerog89
8 months ago by
martinguerrerog89170 wrote:

For those not familiar with the command line and with the JSON query language, here is a fairly simple way to map UUIDS to TCGA barcode ID using R and a canned command in the terminal

The first part is in R

1) Extract the files ID from your manifest file (the one you get from the GDC after you downloaded your data)

setwd("C:/Here/your/manifest/directory")

manifest= "gdc_manifest_20160921_171519.txt" #Manifest name 
x=read.table(manifest,header = T)
manifest_length= nrow(x)
id= toString(sprintf('"%s"', x$id))

2) Create Payload.txt with the commands needed

This commands are extracted from the GDC website https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/

Part1= '{"filters":{"op":"in","content":{"field":"files.file_id","value":[ '


Part2= '] }},"format":"TSV","fields":"file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id","size":'

Part3= paste(shQuote(manifest_length),"}",sep="")



Sentence= paste(Part1,id,Part2,Part3, collapse=" ")



write.table(Sentence,"Payload.txt",quote=F,col.names=F,row.names=F)

The second part is in the command line (CMD or terminal)

cd C:/Here/your/manifest/directory

curl --request POST --header "Content-Type: application/json" --data @Payload.txt "https://gdc-api.nci.nih.gov/files" > File_metadata.txt

Now you should have a file called File_metadata.txt in your working folder with all the data you need

If you get a message:

"'curl' is not recognized as an operable program or batch file."

you should install the cURL library in your computer (if you don't know how to do it, follow this link)

tcga gdc next-gen tutorial R • 2.3k views
ADD COMMENTlink modified 9 days ago • written 8 months ago by martinguerrerog89170

Thank you. It worked for my prostate cancer RNA-seq data.

ADD REPLYlink written 11 weeks ago by morovatunc340

thanks for the post, it was very useful ..

ADD REPLYlink written 9 days ago by juanmafernandezm860
2
gravatar for Chunjie Liu
6 months ago by
Chunjie Liu210
US, Houston
Chunjie Liu210 wrote:

GDC provides API for Curl and HTTPie for command retrieving info through the UUID.

I wrote a simple python script for mapping UUID to TCGA barcode (submitterID). Just input the manifest file downloaded from GDC Data-Portal. Defaul is latest version, you can't use legacy archive UUID to convert through latest version. You may change the endpoint to your version by yourself.

files_endpt = "https://gdc-api.nci.nih.gov/<version>/legacy/<endpoint>"

ADD COMMENTlink written 6 months ago by Chunjie Liu210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 440 users visited in the last hour