From bfdf121ccb4e07fa5723936a4980bdc0ceaad890 Mon Sep 17 00:00:00 2001
From: jykr <jayoung_ryu@g.harvard.edu>
Date: Mon, 25 Mar 2024 15:22:03 -0400
Subject: [PATCH] allow & test feeding no --allele-df-key for tiling run

---
 bean/model/run.py                | 2 +-
 bean/preprocessing/data_class.py | 1 -
 tests/test_run.py                | 4 ++--
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/bean/model/run.py b/bean/model/run.py
index 9615d8a..e09dcd5 100644
--- a/bean/model/run.py
+++ b/bean/model/run.py
@@ -222,7 +222,7 @@ def parse_args():
     parser.add_argument(
         "--allele-df-key",
         type=str,
-        default="allele_counts",
+        default=None,
         help="screen.uns[allele_df_key] will be used as the allele count.",
     )
     parser.add_argument(
diff --git a/bean/preprocessing/data_class.py b/bean/preprocessing/data_class.py
index 4bfc862..ed4a2c3 100644
--- a/bean/preprocessing/data_class.py
+++ b/bean/preprocessing/data_class.py
@@ -567,7 +567,6 @@ def _post_init(
         else:
             allele_counts_selected = self.screen.uns[allele_df_key]
         if control_guide_tag is not None:
-
             def _set_uid_to_row(row):
                 if control_guide_tag in row.guide:
                     row[allele_col].set_uid(row.guide)
diff --git a/tests/test_run.py b/tests/test_run.py
index 1455707..3c877b1 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -120,8 +120,8 @@ def test_run_tiling_with_wo_negctrl_uniform():
 
 
 @pytest.mark.order(24)
-def test_run_tiling_negctrl():
-    cmd = "bean-run sorting tiling tests/data/tiling_mini_screen_annotated.h5ad --scale-by-acc --acc-bw-path tests/data/accessibility_signal.bw -o tests/test_res/tiling/ --allele-df-key allele_counts_spacer_0_19_A.G_translated_prop0.1_0.3 --fit-negctrl --negctrl-col strand --negctrl-col-value neg --control-guide-tag neg --repguide-mask None --n-iter 10"
+def test_run_tiling_negctrl_allelekey():
+    cmd = "bean-run sorting tiling tests/data/tiling_mini_screen_annotated.h5ad --scale-by-acc --acc-bw-path tests/data/accessibility_signal.bw -o tests/test_res/tiling/ --fit-negctrl --negctrl-col strand --negctrl-col-value neg --control-guide-tag neg --repguide-mask None --n-iter 10"
     try:
         subprocess.check_output(
             cmd,