remove reordering of columns to troubleshoot dataset without editing …

…rate
pinellolab · Aug 14, 2024 · 86572bc · 86572bc
1 parent cd294b6
commit 86572bc
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/bean/cli/run.py b/bean/cli/run.py
@@ -123,12 +123,13 @@ def main(args, return_data=False):
     # Build variant dataframe
     adj_negctrl_idx = None
     if args.library_design == "variant":
-        if "edit_rate" not in ndata.screen.guides.columns:
-            ndata.screen.get_edit_from_allele()
-            ndata.screen.get_edit_mat_from_uns(rel_pos_is_reporter=True)
-            ndata.screen.get_guide_edit_rate(
-                unsorted_condition_label=args.control_condition
-            )
+        if not args.uniform_edit:
+            if "edit_rate" not in ndata.screen.guides.columns:
+                ndata.screen.get_edit_from_allele()
+                ndata.screen.get_edit_mat_from_uns(rel_pos_is_reporter=True)
+                ndata.screen.get_guide_edit_rate(
+                    unsorted_condition_label=args.control_condition
+                )
         target_info_df = _get_guide_target_info(
             ndata.screen, args, cols_include=[args.negctrl_col]
         )

diff --git a/bean/model/readwrite.py b/bean/model/readwrite.py
@@ -188,10 +188,6 @@ def write_result_table(
         a_fitted = param_hist_dict["alpha_pi"].detach().cpu().numpy()
         pi = a_fitted[..., 1:].sum(axis=1) / a_fitted.sum(axis=1)
     # guide_info_df["edit_rate_fitted"] = pi
-    guide_info_df = guide_info_df[
-        ["edit_rate"]
-        + [col for col in guide_info_df.columns if col != "Mid" and col != "edit_rate"]
-    ]
     if guide_acc is not None:
         guide_info_df.insert(1, "accessibility", guide_acc)
         scaled_pi = _scale_pi(

diff --git a/bean/model/run.py b/bean/model/run.py
@@ -293,7 +293,10 @@ def _get_guide_info(bdata, args, guide_lfc_pseudocount: int = 5):
             [bdata.guides[["edit_rate", "edit_rate_norm"]], guide_lfc], axis=1
         )
     else:
-        guide_info = pd.concat([bdata.guides[["edit_rate"]], guide_lfc], axis=1)
+        if "edit_rate" in bdata.guides.columns.tolist():
+            guide_info = pd.concat([bdata.guides[["edit_rate"]], guide_lfc], axis=1)
+        else:
+            guide_info = guide_lfc
     return guide_info