fix issue with branch_specific, added check when all genes are filter…

…ed out
LouisFaure · Oct 31, 2024 · fee00c6 · fee00c6
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diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -4,10 +4,11 @@
 Release Notes
 =============
 
-Version 1.0.8 :small:`October 23, 2566/2024`
+Version 1.0.9 :small:`October 31, 2566/2024`
 --------------------------------------------
 - Future proofing scFates by allowing pandas>2.0
 - Fixed most Deprecation warnings.
+- Fix issue with branch_specific, added check when all genes are filtered out
 
 Version 1.0.8 :small:`June 19, 2566/2024`
 --------------------------------------------

diff --git a/scFates/tools/bifurcation_tools.py b/scFates/tools/bifurcation_tools.py
@@ -391,9 +391,12 @@ def branch_specific(
     df = adata.uns[name]["fork"]
 
     df = df[(df.up_A > up_A) & (df.up_p < up_p) & (df.signi_fdr > stf_cut)]
-    df = df[((df.iloc[:, : len(milestones)] + effect) > 0).sum(axis=1) == 1]
+    df = df[((df.iloc[:, : len(milestones)] + effect) >= 0).sum(axis=1) == 1]
     df["branch"] = df.iloc[:, : len(milestones)].idxmax(axis=1)
 
+    if df.shape[0] == 0:
+        raise Exception("The current filtering removed all genes!")
+
     logg.info(
         "    "
         + "branch specific features: "