--- a
+++ b/project_config.py
@@ -0,0 +1,31 @@
+from pathlib import Path
+
+
+#PROJECT_DIR = Path("/home/ema30/zaklab/rare_disease_dx/test_camera_ready") # Path('PATH/TO/SHEPHERD')
+PROJECT_DIR = Path("/n/data1/hms/dbmi/zaklab/mli/rare_disease_diagnosis/test_camera_ready/data/") # Path('PATH/TO/SHEPHERD')
+CURR_KG = '8.9.21_kg' 
+KG_DIR = PROJECT_DIR / 'knowledge_graph' / CURR_KG
+PREDICT_RESULTS_DIR = PROJECT_DIR / 'results'
+SEED = 33
+
+# Modify the following variables for your dataset
+MY_DATA_DIR = Path("simulated_patients")
+MY_TRAIN_DATA = MY_DATA_DIR / f"disease_split_train_sim_patients_{CURR_KG}.txt"
+MY_VAL_DATA = MY_DATA_DIR / f"disease_split_val_sim_patients_{CURR_KG}.txt"
+CORRUPT_TRAIN_DATA = MY_DATA_DIR / f"disease_split_train_sim_patients_{CURR_KG}_phencorrupt.txt"
+CORRUPT_VAL_DATA = MY_DATA_DIR / f"disease_split_val_sim_patients_{CURR_KG}_phencorrupt.txt"
+
+#MY_TRAIN_DATA = MY_DATA_DIR / f"disease_split_all_sim_patients_{CURR_KG}.txt"
+#MY_VAL_DATA = "/n/data1/hms/dbmi/zaklab/mli/rare_disease_diagnosis/test_camera_ready/data/patients/mygene2_patients/mygene2_5.7.22_max250candgenes.txt"
+
+#MY_TEST_DATA = "/n/data1/hms/dbmi/zaklab/mli/rare_disease_diagnosis/test_camera_ready/data/patients/simulated_patients/all_simulated_ddd_mygene2_5.7.22_max20candgenes_phencorrupt.txt"
+
+# Exomiser
+MY_TEST_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_exomiser_distractor_genes_5_candidates_mapped_only_genes.txt" # MY_DATA_DIR / "PATH/TO/YOUR/DATA"
+MY_SPL_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_exomiser_distractor_genes_5_candidates_mapped_only_genes_agg=mean_spl_matrix.npy" #MY_DATA_DIR / "PATH/TO/YOUR/DATA" # Result of data_prep/shortest_paths/add_spl_to_patients.py (suffix: _spl_matrix.npy)
+MY_SPL_INDEX_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_exomiser_distractor_genes_5_candidates_mapped_only_genes_agg=mean_spl_index_dict.pkl" #MY_DATA_DIR / "PATH/TO/YOUR/DATA" # Result of data_prep/shortest_paths/add_spl_to_patients.py (suffix: _spl_index_dict.pkl)
+
+# Curated
+#MY_TEST_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_manual_baylor_nobgm_distractor_genes_5_candidates_mapped_only_genes.txt" # MY_DATA_DIR / "PATH/TO/YOUR/DATA"
+#MY_SPL_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_manual_baylor_nobgm_distractor_genes_5_candidates_mapped_only_genes_agg=mean_spl_matrix.npy" #MY_DATA_DIR / "PATH/TO/YOUR/DATA" # Result of data_prep/shortest_paths/add_spl_to_patients.py (suffix: _spl_matrix.npy)
+#MY_SPL_INDEX_DATA = "/home/ema30/zaklab/rare_disease_dx/formatted_patients/UDN_patients-2022-01-05/all_udn_patients_kg_8.9.21_kgsolved_manual_baylor_nobgm_distractor_genes_5_candidates_mapped_only_genes_agg=mean_spl_index_dict.pkl" #MY_DATA_DIR / "PATH/TO/YOUR/DATA" # Result of data_prep/shortest_paths/add_spl_to_patients.py (suffix: _spl_index_dict.pkl)