This project is to know how drug modalities distributed among subcellular locations using OpenTargets datasets (molecules, Targets, mechanism of action).

Set a virtual environment

python3 -m venv .venv

Activate

source .venv/bin/activate

Install requirements

pip install -r requirements.txt

Run the script

python3 main.py --out_dir /path/to/output/directory

By default, the script downloads the data from OpenTargets API, combines data to "all_combined_data.tsv" and generates significance report in "drugType" and "subcellular_location_label". However if you give "all_combined_data.tsv" as input to --combined_file flag, it continues analysis from that file.

python3 main.py --out_dir /path/to/output/directory --combined_file /path/to/all_combined_data.tsv

To determine the significance for the distribution of drug modalities among subcellular locations, it uses Fisher's exact test and reports in "significance_report.tsv". The final significance_report.tsv , heatmap and barplot will be saved in the --out_dir output directory.

Example Usage:

python3 main.py --combined_file ./all_combined_data.tsv --location_key subcellular_location_label --drug_modality actionType --only_significant

You can also use --only_significant flag to get only significant results in the significance_report.tsv file.

For the --drug_modality flag you can select one of actionType , drugType , targetType , biotype and for the --location_key flag you can select either one of subcellular_location_label , subcellular_location