A script to retrieve data from NCI's GDC data portal to be used by the Xena browser created by UCSC Xena
Both the scripts use gdctools utilities created by Broad Institute. (I did teeny tiny modifications and created some functions)
It will download all files belonging to a particular data type in all Project IDs present in a Project. All files will be downloaded in a folder.
sample_one.py
This file labels the columns according to the file name.
sample_two.py
This file labels the columns according to the submitter id, ex: TCGA-AB-C123
A folder will be created for each Project ID and inside that folder 10 files will be downloaded for each work-flow type specified. The folder will also contain a summary of all the files downloaded in the form of TSVs in a text file.
The file structure looks something like this:
* Data
* TCGA-BRCA
* HTSeq - FPKM
* file1.txt.gz
* file2.txt.gz
* HTSeq - FPKM-UQ
* file1.txt.gz
* file2.txt.gz
* HTSeq - FPKM.txt
* HTSeq - FPKM-UQ.txt
* TCGA-UCEC
* TCGA-KIRC
* TCGA-LUAD
you can download the necessary modules using pip
pip install -r requirements.txt