save data file as .pkl output, only when fed with --save-raw

CHANGELOG.md

@@ -1,9 +1,9 @@
 # Changelog
-## 1.2.5
-* Allow `bean run .. tiling` for untranslated `--allele-df-key`.
-
+## 1.2.8
+* Change .pyx files to be compatible with more recent numpy versions
+## 1.2.7
+* **CRITICAL** Fix sample ordering & masking issue for survival screens
 ## 1.2.6
 * Fix overflow in `bean run survival` and autograde error related to inplace assignment for `bean run survival tiling`.
-
-## 1.2.7
-* **CRITICAL** Fix sample ordering & masking issue for survival screens
+## 1.2.5
+* Allow `bean run .. tiling` for untranslated `--allele-df-key`.

bean/cli/run.py

@@ -211,15 +211,20 @@ def main(args):
             )
         else:
             param_history_dict_negctrl = None
+        save_dict["data"] = ndata
+    # Save results
 
     outfile_path = (
         f"{prefix}/bean_element[sgRNA]_result.{model_label}{args.result_suffix}.csv"
     )
     info(f"Done running inference. Writing result at {outfile_path}...")
     if not os.path.exists(prefix):
         os.makedirs(prefix)
-    with open(f"{prefix}/{model_label}.result{args.result_suffix}.pkl", "wb") as handle:
-        pkl.dump(save_dict, handle)
+    if args.save_raw:
+        with open(
+            f"{prefix}/{model_label}.result{args.result_suffix}.pkl", "wb"
+        ) as handle:
+            pkl.dump(save_dict, handle)
     write_result_table(
         target_info_df,
         param_history_dict,

bean/model/parser.py

@@ -224,5 +224,10 @@ def parse_args(parser=None):
         action="store_true",
         help="Load existing .pkl file if present.",
     )
+    parser.add_argument(
+        "--save-raw",  # TODO: add check args
+        action="store_true",
+        help="Write .pkl file with raw input/output.",
+    )
 
     return parser