Welcome to the DMS_a-syn repository! This project focuses on the descriptive data analysis for modeling alpha-synuclein Deep Mutation Scan (DMS) data. It was developed as part of a bioinformatics class project at the University of Texas at Austin. My team was composed of Nathan Strominger and me.
These instructions will guide you through setting up your local environment and running the analysis.
Before you begin, ensure you have Python installed on your machine. This project was developed using Python 3.8. We recommend using a virtual environment to manage the dependencies.
- Clone the repository:
# clone the repository
git clone https://github.com/yourusername/DMS_a-syn.git
cd DMS_a-syn
# creates a vitual enviroment
python -m venv env
source env/bin/activate
# install the required packages
pip install -r requirements.txtTo run the analysis and extract embeddings for your protein data, follow these steps:
All the steps on how to preprocessing the data and the modeling is described on 'data_processing.ipynb'
Extract embeddings: Replace model_name with the name of the model you are using, and fasta_file with the path to your FASTA file containing protein sequences.
python scripts/extract.py esm2_t30_150M_UR50D data/a_syn_DMS_sequences.fasta embeddings/output_folder_name 30 --include mean