conda create -n epam python=3.11
conda activate epam
conda install datrie
make install
The netam package needs to be installed within the epam conda environment (though outside the epam file directory). Separately clone the repository (https://github.com/matsengrp/netam), checkout the relevant version of the repo git checkout 22c8873, and run make install.
Getting Thrifty model crepes:
git submodule init
git submodule update
scp <username>@quokka:/fh/fast/matsen_e/shared/bcr-mut-sel/working/crepe/2024-12-08-thrifty-prod/cnn_ind_lrg-v1wyatt-simple-0* thrifty-models/models/
Getting GCReplay-DMS data:
mkdir data/gcreplay
scp <username>@quokka:/fh/fast/matsen_e/ksung2/epam-gcreplay/final_variant_scores.csv data/gcreplay/
scp <username>@quokka:/fh/fast/matsen_e/ksung2/epam-gcreplay/chigy_?c_mutation_rates_nt.csv data/gcreplay/
Getting S5F data:
scp -r <username>@quokka:/fh/fast/matsen_e/ksung2/shmple-gpu/shmple/model_weights/S5F data/
- An "aaprob" matrix is a matrix that expresses the probability of various child amino acid substitutions for each site, laid out with sites on the rows and amino acids on the columns.
Running it to get matrices:
epam aaprob NetamSHM '{"model_path_prefix": "/fh/fast/matsen_e/shared/bcr-mut-sel/netam-shm/trained_models/cnn_ind_med-shmoof_small-full-0"}' _ignore/wyatt-10x-1p5m_pcp_2023-09-11.first100.csv _ignore/output.hdf5