gdc-scan

This utility aims to provide a programmatic interface to the GDC API.

usage

gdc-scan provides a command tree to access the GDC API. Here is a quick tree of the available commands:

projects
├── list
└── mapping
cases
├── list
├── files
└── mapping
files
├── list
├── facets
├── download
└── mapping

So for instance, to find a list of all projects on the GDC you can invoke:

python gdc-scan.py projects list

Other commands take optional arguments, for instance:

python gdc-scan.py files download --format MAF --project TCGA-PAAD

The mapping commands tell you every property available from GDC for that particular category.

projects

cases

files

find all data types

In order to find all data types stored in the GDC, you can use the facets command:

python gdc-scan.py files facets data_type

Current output for this:

{"data_type": {"Copy Number Segment": 22376, "Clinical Supplement": 11168, "Masked Somatic Mutation": 33, "Annotated Somatic Mutation": 45577, "Masked Copy Number Segment": 22376, "miRNA Expression Quantification": 11488, "Aligned Reads": 45988, "Aggregated Somatic Mutation": 144, "Isoform Expression Quantification": 11488, "Gene Expression Quantification": 34722, "Raw Simple Somatic Mutation": 45577, "Biospecimen Supplement": 11356}}

download all files of a given type

Then, you can download all files of a given type (say, "Gene Expression Quantification") with the following command:

python gdc-scan.py files download --type "Gene Expression Quantification"

find the file_id and submitter_id for each file of a given type

Say you want to get all the submitter_ids for all of the legacy BAM files in the system. Here is the command for that:

python gdc-scan.py files list --type "Aligned reads" --key file_id,submitter_id --legacy

This will return a list of dictionaries with the keys provided. If you want to find out all of the possible keys you could use, try mapping:

python gdc-scan.py files mapping