conda env create -f environment.yaml
conda activate vaxseer
MMseq2 is required for aligning sequences.
In data/readme.md.
Models are available here.
One could also run the following code to download specific models:
# task: lm (dominance predictor) or/and hi (antigenicity predictor)
# year: from 2012 to 2021
# subtype: a_h3n2 or/and a_h1n1
python download_models_from_dropbox.py --task lm --year 2012 --subtype a_h3n2 --output_dir runs
# To download all models (around 60GB):
python download_models_from_dropbox.py
Results are available here.
wget https://people.csail.mit.edu/wxsh/vaxseer/results.tar.gz
tar -zxvf results.tar.gz