A simple Python script to detect and report breast cancer-associated genes and their aliases.
- 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.
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:
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
$ conda env create --name {environment-name} --file environment.yml
$ source activate {environment-name}
$ python detect_breast_cancer_genes.py
$ source deactivate
Alternatively, to run the script as a stand-alone, make sure the following dependencies are included:
- Python version 3
- Pip
- Matplotlib
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.