add evidence metrics to output

bean/preprocessing/utils.py

@@ -228,3 +228,14 @@ def _obtain_effective_edit_rate(ndata, count_thres=10):
 
 def _obtain_n_guides_alleles_per_variant(ndata):
     return (ndata.allele_to_edit.sum(axis=1) > 0).sum(axis=0)
+
+
+def _obtain_n_cooccurring_variants(ndata) -> np.ndarray:
+    """Obtain the number of co-occurring variants in any allele produced by any guides."""
+    allele_to_edit = ndata.allele_to_edit.cpu()
+    n_coedited_vars_edits = []
+    for edit_idx in range(allele_to_edit.shape[-1]):
+        gidx, aidx = torch.where(allele_to_edit[:, :, edit_idx] > 0)
+        n_coedited_vars = (allele_to_edit[gidx, aidx, :].sum(axis=0) > 0).sum() - 1
+        n_coedited_vars_edits.append(n_coedited_vars)
+    return np.array(n_coedited_vars_edits)

bin/bean-run

@@ -24,6 +24,7 @@ from bean.preprocessing.data_class import (
 from bean.preprocessing.utils import (
     _obtain_effective_edit_rate,
     _obtain_n_guides_alleles_per_variant,
+    _obtain_n_cooccurring_variants,
 )
 
 import bean as be
@@ -196,6 +197,7 @@ def main(args, bdata):
         )
         target_info_df["effective_edit_rate"] = _obtain_effective_edit_rate(ndata).cpu()
         target_info_df["n_guides"] = _obtain_n_guides_alleles_per_variant(ndata).cpu()
+        target_info_df["n_coocc"] = _obtain_n_cooccurring_variants(ndata)
         if args.adjust_confidence_by_negative_control:
             adj_negctrl_idx = np.where(target_info_df.ref == target_info_df.alt)[0]
             print("syn idx: ", adj_negctrl_idx)

tests/test_run.py

@@ -0,0 +1,80 @@
+import pytest
+import subprocess
+
+
+@pytest.mark.order(13)
+def test_run_variant_wacc():
+    cmd = "bean-run variant tests/data/var_mini_screen_annotated.h5ad --scale-by-acc --acc-bw-path tests/data/accessibility_signal_var.bw -o tests/test_res/var/ --repguide-mask None"
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc
+
+
+@pytest.mark.order(14)
+def test_run_variant_noacc():
+    cmd = "bean-run variant tests/data/var_mini_screen_annotated.h5ad -o tests/test_res/var/ "
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc
+
+
+@pytest.mark.order(15)
+def test_run_variant_wo_negctrl_uniform():
+    cmd = "bean-run variant tests/data/var_mini_screen_annotated.h5ad -o tests/test_res/var/ --uniform-edit "
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc
+
+
+@pytest.mark.order(16)
+def test_run_tiling_wo_negctrl():
+    cmd = "bean-run 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 --control-guide-tag None  --repguide-mask None"
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc
+
+
+@pytest.mark.order(17)
+def test_run_tiling_with_wo_negctrl_noacc():
+    cmd = "bean-run tiling tests/data/tiling_mini_screen_annotated.h5ad -o tests/test_res/tiling/ --allele-df-key allele_counts_spacer_0_19_A.G_translated_prop0.1_0.3 --control-guide-tag None  --repguide-mask None"
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc
+
+
+@pytest.mark.order(18)
+def test_run_tiling_with_wo_negctrl_uniform():
+    cmd = "bean-run tiling tests/data/tiling_mini_screen_annotated.h5ad -o tests/test_res/tiling/ --uniform-edit --allele-df-key allele_counts_spacer_0_19_A.G_translated_prop0.1_0.3 --control-guide-tag None  --repguide-mask None"
+    try:
+        subprocess.check_output(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise exc