fix: out_dir => outdir

predict_chromosome.py

@@ -216,7 +216,7 @@ def predict_and_write(
     start_time = time.time()
 
     denoised_anchor_to_anchor.to_csv(
-        os.path.join(out_dir, chromosome + ".denoised.anchor.to.anchor"),
+        os.path.join(outdir, chromosome + ".denoised.anchor.to.anchor"),
         sep="\t",
         index=False,
         header=False,
@@ -242,7 +242,7 @@ if __name__ == "__main__":
         help="path to model architecture .json file (by default it is assumed to be the same as the weights file)",
     )
     parser.add_argument(
-        "--out_dir",
+        "--outdir",
         type=str,
         help="directory where the output interaction file will be stored",
     )
@@ -299,7 +299,7 @@ if __name__ == "__main__":
         json_file = args.json_file
     else:
         json_file = args.h5_file.replace("h5", "json")
-    out_dir = args.out_dir
+    outdir = args.outdir
     anchor_dir = args.anchor_dir
     chromosome = args.chromosome
     small_matrix_size = args.small_matrix_size
@@ -309,7 +309,7 @@ if __name__ == "__main__":
     val_cols = args.val_cols
     keep_zeros = args.keep_zeros
 
-    os.makedirs(out_dir, exist_ok=True)
+    os.makedirs(outdir, exist_ok=True)
 
     with open(json_file, "r") as f:
         model = model_from_json(f.read())  # load model
@@ -318,7 +318,7 @@ if __name__ == "__main__":
         model,
         full_matrix_dir,
         input_name,
-        out_dir,
+        outdir,
         anchor_dir,
         chromosome,
         small_matrix_size,