tf binding debugged

Author: janursa

scripts/sync_resources.sh

@@ -25,7 +25,8 @@ set -e
 # aws s3 sync  resources/extended_data/ s3://openproblems-data/resources/grn/extended_data --delete
 # aws s3 sync resources/results/experiment  s3://openproblems-data/resources/grn/results/experiment --delete 
 # aws s3 sync resources_test  s3://openproblems-data/resources_test/grn/ --delete 
-aws s3 sync  s3://openproblems-data/resources_test/grn/ resources_test --delete 
+# aws s3 sync  s3://openproblems-data/resources_test/grn/ resources_test --delete 
+aws s3 sync  s3://openproblems-data/resources/grn/grn_benchmark/ground_truth resources_test/grn_benchmark/ground_truth
 # aws s3 sync  resources/grn_benchmark/ground_truth s3://openproblems-data/resources/grn/grn_benchmark/ground_truth 
 # aws s3 sync  resources/grn_benchmark/ s3://openproblems-data/resources/grn/grn_benchmark/ --delete
 

src/metrics/gs_recovery/script.py

@@ -49,3 +49,4 @@
     dataset_id = ad.read_h5ad(par['evaluation_data'], backed='r').uns['dataset_id']
     method_id = ad.read_h5ad(par['prediction'], backed='r').uns['method_id']
     format_save_score(output, method_id, dataset_id, par['score'])
+    print(par['score'])

src/metrics/tf_binding/script.py

@@ -19,10 +19,11 @@
     'output_detailed_metrics': True
 }
 ## VIASH END
-
+local_run = False
 try:
     sys.path.append(meta["resources_dir"])
 except:
+    local_run=True
     meta = {
     "resources_dir":'src/metrics/experimental/tf_binding/',
     "util_dir": 'src/utils',
@@ -32,15 +33,15 @@
 from helper import main as main 
 from util import format_save_score, parse_args
 
-args = parse_args(par)
+if local_run:
+    par = parse_args(par)
 
 
 if __name__ == "__main__":
-    output = main(par)
-    print(output)
+    df = main(par)
 
     dataset_id = ad.read_h5ad(par['evaluation_data'], backed='r').uns['dataset_id']
     method_id = ad.read_h5ad(par['prediction'], backed='r').uns['method_id']
 
-    score_adata = format_save_score(output, dataset_id, method_id, par['score'])
-    print('Completed', flush=True)
+    format_save_score(df, dataset_id, method_id, par['score'])
+    print('Completed', flush=True)

src/utils/dataset_config.env

@@ -19,7 +19,7 @@ METRICS_replogle="regression,ws_distance,tf_recovery,tf_binding,sem,gs_recovery"
 METRICS_adamson="regression,tf_binding,sem,gs_recovery"
 METRICS_norman="regression,ws_distance,tf_binding,sem,gs_recovery"
 METRICS_nakatake="regression,sem,gs_recovery"
-METRICS_op="gs_recovery"
+METRICS_op="gs_recovery,tf_binding"
 METRICS_300BCG="regression,vc,rc_tf_act,tf_binding,sem,gs_recovery"
 METRICS_ibd_uc="regression,vc,tf_binding,sem,gs_recovery"
 METRICS_ibd_cd="regression,vc,tf_binding,sem,gs_recovery"