Variant extraction from papers

Install

Create a virtual environment with Python-3.9 (only once):

python3 -m venv venv
Activate the virtual environment each time:

source venv/bin/activate
Install dependencies (only once):

pip install -r requirements.txt

Train model (only once)

Download nltk and related tools, prepare data for training and train model:

bash train_model.sh

Configure credentials

Edit:

utils/all_config.cfg

With wbtools access credentials

Tests

To test regexes:

python test_regexes.py

To fetch some papers locally:

python fetch_papers.py

To test the variant extraction on some papers

python hybrid_extraction.py

Execution

python main.py