krademaker / detect-breast-cancer-genes

A simple Python script to detect and report breast cancer genes.

Detect Breast Cancer Genes

A simple Python script to detect and report breast cancer-associated genes and their aliases.

How it works

• Provided with a file containing 8159 known human cancer genes, the script searches for breast cancer related terms in the gene description with a regular expression.
• Matching genes and aliases are returned to the console.
• Aliases for genes and number of alias occurrences are plotted.

To use a custom file, make sure it matches the tab-separated format of the file included to this repository.

Getting started

Running in an environment

It's recommended to run the script in a contained Conda environment to ensure the installation of all dependencies, the required steps are listed below:

Install Miniconda

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

$ bash Miniconda3-latest-Linux-x86_64.sh

Create and activate the environment

$ conda env create --name {environment-name} --file environment.yml

$ source activate {environment-name}

Run the script

$ python detect_breast_cancer_genes.py

$ source deactivate

Running stand-alone

Alternatively, to run the script as a stand-alone, make sure the following dependencies are included:

• Python version 3
• Pip
• Matplotlib

Examples

1 - Console output returns breast cancer-associated genes and their aliases.

2 - Chart plots number of aliases per breast cancer-associated gene.

3 - Chart plots number of occurrences of aliases.