cBioPortal Command Line Utilities

Description

cBioPortal Command Line Utilities is project focused on providing simple command line tools for retrieving cancer genomic data using a web API and summarizing the results.

Intstallation

Python Package Dependencies

• requests

To install this package run the following command:

$ pip install requests

If that fails you may need to refer to the PIP documentation.

Background

This project utilize the cBioPortal web API. For more information on the project see the documentation.

Getting started

Example: getting summary results for gene TP53

To run this analysis the following command can be used:

$ python gbm_summarize.py TP53

The command should return results in the following format:

TP53 is copy number altered in 23% of all cases.
TP53 is mutated in 29% of all cases.

Example: getting summary results for multiple genes: TP53, MDM4, MDM2

To run this analysis the following command can be used:

$ python gbm_summarize.py TP53 MDM2 MDM4

The command should return results in the following format:

Total % of cases where MDM4 is altered by either mutation or copy number alteration: 50% of all cases.
Total % of cases where MDM2 is altered by either mutation or copy number alteration: 40% of all cases.
Total % of cases where TP53 is altered by either mutation or copy number alteration: 30% of all cases.