tf bug in regression fixed

openproblems-bio · Aug 29, 2024 · 144813f · 144813f
1 parent facb2c6
commit 144813f
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
@@ -47,7 +47,7 @@ functionality:
       direction: input 
       required: false
       example: collectri
-    - name: --tfs
+    - name: --tf_all
       type: file
       direction: input
       default: 'resources/prior/tf_all.csv'

diff --git a/src/metrics/regression_1/main.py b/src/metrics/regression_1/main.py
@@ -173,7 +173,7 @@ def main(par):
     print('Reading input files', flush=True)
 
     perturbation_data = ad.read_h5ad(par['perturbation_data'])
-    tf_all = np.loadtxt(par['tfs'], dtype=str)
+    tf_all = np.loadtxt(par['tf_all'], dtype=str)
     gene_names = perturbation_data.var.index.to_numpy()
     net = pd.read_csv(par['prediction'])
     # subset to keep only those links with source as tf

diff --git a/src/metrics/regression_2/main.py b/src/metrics/regression_2/main.py
@@ -277,7 +277,7 @@ def main(par: Dict[str, Any]) -> pd.DataFrame:
     n_features_theta_max = np.asarray([data[gene_name]['1'] for gene_name in gene_names], dtype=int)
 
     # Load list of putative TFs
-    df = pd.read_csv(par['tfs'], header=None, names=['gene_name'])
+    df = pd.read_csv(par['tf_all'], header=None, names=['gene_name'])
     tf_names = set(list(df['gene_name'].to_numpy()))
 
     # Evaluate GRN