debug errors in calculating edits

pinellolab · Aug 26, 2024 · 3b40968 · 3b40968
1 parent e5b3a90
commit 3b40968
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Showing 5 changed files with 10 additions and 9 deletions.
diff --git a/bean/cli/count.py b/bean/cli/count.py
@@ -70,6 +70,7 @@ def main(args):
         counter.screen.uns["allele_counts"] = counter.screen.uns["allele_counts"].loc[
             counter.screen.uns["allele_counts"].allele.map(str) != "", :
         ]
+        counter.screen.get_edit_from_allele("allele_counts", "allele")
         if match_target_pos:
             counter.screen.get_edit_mat_from_uns(target_base_edits, match_target_pos)
         else:

diff --git a/bean/cli/count_samples.py b/bean/cli/count_samples.py
@@ -47,7 +47,9 @@ def count_sample(R1: str, R2: str, sample_id: str, args: argparse.Namespace):
     except KeyError as e:
         raise KeyError(args_dict["edited_base"]) from e
 
-    match_target_pos = args_dict["match_target_pos"]
+    match_target_pos = (
+        args_dict["match_target_pos"] if not args_dict["tiling"] else False
+    )
     if (
         "guide_start_seqs_tbl" in args_dict
         and args_dict["guide_start_seqs_tbl"] is not None

diff --git a/bean/framework/ReporterScreen.py b/bean/framework/ReporterScreen.py
@@ -410,7 +410,7 @@ def get_edit_mat_from_uns(
         edits["guide_start_pos"] = (
             reporter_length
             - reporter_right_flank_length
-            - guide_len[edits.guide_idx].reset_index(drop=True)
+            - guide_len.iloc[edits.guide_idx].reset_index(drop=True)
         )
         if not match_target_position:
             edits["rel_pos"] = edits.edit.map(lambda e: e.rel_pos)

diff --git a/bean/preprocessing/data_class.py b/bean/preprocessing/data_class.py
@@ -223,10 +223,10 @@ def transform_data(self, X, n_bins=None):
                 .T.reshape((self.n_reps, n_bins, self.n_guides))
                 .float()
             )
-        except RuntimeError:
+        except RuntimeError as e:
             print((self.n_reps, n_bins, self.n_guides))
             print(X.shape)
-            exit(1)
+            raise e
         if self.device is not None:
             x = x.cuda()
         return x
@@ -347,9 +347,7 @@ def _post_init(
                 ]
                 edited_control = self.transform_data(screen_t.layers["edits"], n_bins=1)
                 nonedited_control = (
-                    self.transform_data(
-                        screen_t.layers["X_bcmatch"], len(self.control_condition)
-                    )
+                    self.transform_data(screen_t.layers["X_bcmatch"], n_bins=1)
                     - edited_control
                 )
                 nonedited_control[nonedited_control < 0] = 0

diff --git a/tests/test_count.py b/tests/test_count.py
@@ -110,7 +110,7 @@ def test_barcode_start_idx():
 
 @pytest.mark.order(108)
 def test_count_samples_tiling():
-    cmd = "bean count-samples -i tests/data/sample_list_tiling.csv -b A -f tests/data/test_guide_info_tiling_chrom.csv -o tests/test_res/tiling/ -r"
+    cmd = "bean count-samples -i tests/data/sample_list_tiling.csv -b A -f tests/data/test_guide_info_tiling_chrom.csv -o tests/test_res/tiling/ -r --tiling"
     try:
         subprocess.check_output(
             cmd,
@@ -123,7 +123,7 @@ def test_count_samples_tiling():
 
 @pytest.mark.order(109)
 def test_count_chroms():
-    cmd = "bean count --R1 tests/data/test_tiling_R1.fastq --R2 tests/data/test_tiling_R2.fastq -b A -f tests/data/test_guide_info_tiling_chrom.csv -o tests/test_res/tiling_chrom/ -r"
+    cmd = "bean count --R1 tests/data/test_tiling_R1.fastq --R2 tests/data/test_tiling_R2.fastq -b A -f tests/data/test_guide_info_tiling_chrom.csv -o tests/test_res/tiling_chrom/ -r --tiling"
     try:
         subprocess.check_output(
             cmd,