From 67a37865e5f5af8897ae1afc10916f0ecf1ac18e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Johansson?= <bjorn_johansson@bio.uminho.pt>
Date: Mon, 10 Mar 2025 14:01:25 +0000
Subject: [PATCH] Retain letter_annotation as None in upper and lower methods
 (#4966)

* gitignore .python-version
* added name & email
* fix so that _per_letter_annotations is not set by calling upper or lower methods
* added test for initiation of SeqRecord checking the __dict__ and a test for the __dict__ created by upper
---
 .gitignore              |  6 ++++++
 Bio/SeqRecord.py        | 12 ++++++++++--
 CONTRIB.rst             |  1 +
 Tests/test_SeqRecord.py | 29 +++++++++++++++++++++++++++++
 4 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 2f8a2c8d8..19d579278 100644
--- a/.gitignore
+++ b/.gitignore
@@ -134,3 +134,9 @@ ENV/
 
 # Testing
 **/.coverage
+
+# Ignore the .python-version file used by pyenv
+# This file specifies the Python version for a project,
+# but should not be committed to Git, as different developers
+# may use different Python versions.
+.python-version
diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
index 739942d75..648d3c51e 100644
--- a/Bio/SeqRecord.py
+++ b/Bio/SeqRecord.py
@@ -1127,7 +1127,11 @@ class SeqRecord:
             dbxrefs=self.dbxrefs[:],
             features=self.features[:],
             annotations=self.annotations.copy(),
-            letter_annotations=self.letter_annotations.copy(),
+            letter_annotations=(
+                None
+                if self._per_letter_annotations is None
+                else self.letter_annotations.copy()
+            ),
         )
 
     def lower(self) -> "SeqRecord":
@@ -1174,7 +1178,11 @@ class SeqRecord:
             dbxrefs=self.dbxrefs[:],
             features=self.features[:],
             annotations=self.annotations.copy(),
-            letter_annotations=self.letter_annotations.copy(),
+            letter_annotations=(
+                None
+                if self._per_letter_annotations is None
+                else self.letter_annotations.copy()
+            ),
         )
 
     def isupper(self):
diff --git a/CONTRIB.rst b/CONTRIB.rst
index 5fc55b186..41e35b942 100644
--- a/CONTRIB.rst
+++ b/CONTRIB.rst
@@ -66,6 +66,7 @@ please open an issue on GitHub or mention it on the mailing list.
 - Bertrand Frottier <bertrand.frottier at domain free.fr>
 - Bertrand Néron <https://github.com/bneron>
 - Bill Barnard <bill at domain barnard-engineering.com>
+- Björn Johansson <bjorn_johansson@bio.uminho.pt>
 - Blaise Li <https://github.com/blaiseli>
 - Bob Bussell <rgb2003 at domain med.cornell.edu>
 - Bogdan T. <bogdan at pearlgen dot com>
diff --git a/Tests/test_SeqRecord.py b/Tests/test_SeqRecord.py
index f6ad5fe2e..cfb45fa8e 100644
--- a/Tests/test_SeqRecord.py
+++ b/Tests/test_SeqRecord.py
@@ -133,6 +133,21 @@ class SeqRecordCreation(unittest.TestCase):
         with self.assertRaises(TypeError):
             SeqRecord(Seq("ACGT"), features={})
 
+    def test_default_properties(self):
+        seqobj = Seq("A")
+        default__dict__ = {
+            "_seq": seqobj,
+            "id": "<unknown id>",
+            "name": "<unknown name>",
+            "description": "<unknown description>",
+            "dbxrefs": [],
+            "annotations": {},
+            "_per_letter_annotations": None,
+            "features": [],
+        }
+        bsr = SeqRecord(seqobj)
+        self.assertEqual(bsr.__dict__, default__dict__)
+
 
 class SeqRecordMethods(unittest.TestCase):
     """Test SeqRecord methods."""
@@ -226,6 +241,20 @@ Seq('ABCDEFGHIJKLMNOPQRSTUVWZYX')"""
 
     def test_upper(self):
         self.assertEqual("ABCDEFGHIJKLMNOPQRSTUVWZYX", self.record.lower().upper().seq)
+        seqobj = Seq("A")
+        default__dict__ = {
+            "_seq": seqobj,
+            "id": "<unknown id>",
+            "name": "<unknown name>",
+            "description": "<unknown description>",
+            "dbxrefs": [],
+            "annotations": {},
+            "_per_letter_annotations": None,
+            "features": [],
+        }
+        bsr = SeqRecord(seqobj)
+        bsru = bsr.upper()
+        self.assertEqual(bsru.__dict__, default__dict__)
 
     def test_lower(self):
         self.assertEqual("abcdefghijklmnopqrstuvwzyx", self.record.lower().seq)