fix string to allele conversion

pinellolab · Oct 16, 2023 · ed99b29 · ed99b29
1 parent 3205411
commit ed99b29
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/bean/framework/Edit.py b/bean/framework/Edit.py
@@ -68,7 +68,7 @@ def from_str(cls, edit_str):  # pos:strand:start>end
     def match_str(cls, edit_str):
         if isinstance(edit_str, Edit):
             return True
-        pattern = r"((chr)?\d+:)?-?\d+:-?\d+:[+-]:[A-Z*-]>[A-Z*-]"
+        pattern = r"(((chr)?\d+|nan):)?-?\d+:-?\d+:[+-]:[A-Z*-]>[A-Z*-]"
         pattern2 = r"[\w*]!-?\d+:-?\d+:[+-]:[A-Z*-]>[A-Z*-]"
         return re.fullmatch(pattern, edit_str) or re.fullmatch(pattern2, edit_str)
 
@@ -151,9 +151,11 @@ def from_str(cls, allele_str):  # pos:strand:start>end
             for edit_str in allele_str.split(","):
                 edit = Edit.from_str(edit_str)
                 edits.add(edit)
-        except ValueError:
+        except ValueError as e:
             if allele_str.strip() == "":
                 return cls(None)
+            else:
+                raise e
         return cls(edits)
 
     @classmethod

diff --git a/bean/framework/ReporterScreen.py b/bean/framework/ReporterScreen.py
@@ -906,7 +906,10 @@ def concat(screens: Collection[ReporterScreen], *args, axis=1, **kwargs):
 
             if max(len(screen_uns_df) for screen_uns_df in screen_uns_dfs) == 0:
                 continue
-            merge_on = screen[0].uns[k].columns[:2].tolist()
+            if "guide_reporter_allele" in k:
+                merge_on = screen[0].uns[k].columns[:3].tolist()
+            else:
+                merge_on = screen[0].uns[k].columns[:2].tolist()
             try:
                 edit_cls = type(screens[0].uns[k][merge_on[1]][0])
             except IndexError:
@@ -920,7 +923,7 @@ def concat(screens: Collection[ReporterScreen], *args, axis=1, **kwargs):
             for i, screen in enumerate(screens):
                 if screen.uns[k][merge_on].duplicated().any():
                     raise ValueError(
-                        f"{i}-th ReporterScreen .uns['{k}'] has duplicated row. Aborting."
+                        f"{i}-th ReporterScreen .uns['{k}'] has duplicated row. Aborting.: {screen.uns[k][merge_on].loc[screen.uns[k][merge_on].duplicated()]}"
                     )
                 if i == 0:
                     adata.uns[k] = screen.uns[k]