From 3691df4c2bfdab29b61be53a6171ed0cb06bf5fc Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 30 Jan 2026 12:13:06 -0600
Subject: Fix bug in reading file: Ensure to read all lines.

---
 scripts/phenotypes/delete_phenotypes.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/scripts/phenotypes/delete_phenotypes.py b/scripts/phenotypes/delete_phenotypes.py
index 028f061..e1396f3 100644
--- a/scripts/phenotypes/delete_phenotypes.py
+++ b/scripts/phenotypes/delete_phenotypes.py
@@ -26,10 +26,11 @@ def read_xref_ids_file(filepath: Optional[Path]) -> tuple[int, ...]:
 
     _ids: tuple[int, ...] = tuple()
     with filepath.open(mode="r") as infile:
-        try:
-            _ids += (int(infile.readline().strip()),)
-        except TypeError:
-            pass
+        for line in infile.readlines():
+            try:
+                _ids += (int(line.strip()),)
+            except TypeError:
+                pass
 
     return _ids
 
-- 
cgit 1.4.1