# Bash script to run SHEPHERD to generate predictions

# Command to run this bash script:

# bash predict.sh

# IMPORTANT

#    - To generate predictions on your own dataset (default), please use --patient_data my_data

#    - To generate predictions on simulated test patients, please use --patient_data test_predict

# Command to run the predict script for each task. Comment out tasks you don't want to generate predictions for. 

python predict.py \

--run_type causal_gene_discovery \

--patient_data test_predict \

--edgelist KG_edgelist_mask.txt \

--node_map KG_node_map.txt \

--saved_node_embeddings_path checkpoints/pretrain.ckpt \

--best_ckpt checkpoints/causal_gene_discovery.ckpt

python predict.py \

--run_type patients_like_me \

--patient_data my_data \

--edgelist KG_edgelist_mask.txt \

--node_map KG_node_map.txt \

--saved_node_embeddings_path checkpoints/pretrain.ckpt \

--best_ckpt checkpoints/patients_like_me.ckpt

python predict.py \

--run_type disease_characterization \

--patient_data my_data \

--edgelist KG_edgelist_mask.txt \

--node_map KG_node_map.txt \

--saved_node_embeddings_path checkpoints/pretrain.ckpt \

--best_ckpt checkpoints/disease_characterization.ckpt