query_tcga

author: Jacki Novik

Overview

Helper functions to download TCGA data from GDC

Installation / Usage

To install, clone the repo & edit the default values:

$ git clone https://github.com/jburos/query_tcga.git
$ vim query_tcga/query_tcga/defaults.py
$ python setup.py install

Or, install from git via pip:

$ pip install git+git://github.com/jburos/query_tcga

Setup

There are a few steps you will have to follow before using this code.

• Install gdc-client.
  • Install per the instructions
  • Edit the variable GDC_CLIENT_PATH by one of the methods described below
• Log into GDC, request access to TCGA & download an auth-token
  1. Gain authorization
  2. Download the authentication token
  3. Edit the variable GDC_TOKEN_PATH by one of the methods described below

Once you have these items set up, you can use this package to download and/or parse clinical, WXS, VCF and other files from the GDC portal by project.

Configuration

Because many of the files available via the GDC require authentication, some configuration settings are required in order to use this package.

Only one setting is required to be set by the user: GDC_TOKEN_PATH. The other setting (GDC_CLIENT_PATH) is strongly recommended.

These and all settings can be configured in one of two ways:

1. Via a config.ini file, loaded in via config.load_config()
2. In Python code, updating value via config.set_value()

If you choose to use a config file, options should be included under [main], like so:

**Example config.ini file **

[main]
GDC_TOKEN_PATH = /full/path/to/your/gdc_token_file.txt
GDC_CLIENT_PATH = /usr/local/bin/gdc-client

This can be loaded into a python script as:

from query_tcga import config

config.load_config('config.ini')

Example

See the companion repo (tcga-blca) for example usage.

Contributing

TBD

Testing

Test cases for query_tcga are written in pytest.

For example, you can run test cases as follows:

python -m pytest tests --exitfirst -v