fix: Sort transcript data output

src/cool_seq_tool/mappers/mane_transcript.py

@@ -1374,11 +1374,12 @@ async def grch38_to_mane_c_p(
         mane_transcripts = set()  # Used if getting longest compatible remaining
         for current_mane_data in mane_data:
             mane_c_ac = current_mane_data["RefSeq_nuc"]
+            mane_alt_ac = current_mane_data["GRCh38_chr"]
             mane_transcripts |= {mane_c_ac, current_mane_data["Ensembl_nuc"]}
 
             # GRCh38 -> MANE C
             mane_tx_genomic_data = await self.uta_db.get_mane_c_genomic_data(
-                mane_c_ac, None, start_pos, end_pos
+                ac=mane_c_ac, alt_ac=mane_alt_ac, start_pos=start_pos, end_pos=end_pos
             )
             if not mane_tx_genomic_data:
                 continue

src/cool_seq_tool/sources/uta_database.py

@@ -543,7 +543,8 @@ async def get_mane_c_genomic_data(
         self, ac: str, alt_ac: str | None, start_pos: int, end_pos: int
     ) -> GenomicTxMetadata | None:
         """Get MANE transcript and genomic data. Used when going from g. to MANE c.
-        representation.
+        representation. This function parses queried data from the tx_exon_aln_v
+        table, and sorts the queried data by the most recent genomic build
 
         >>> import asyncio
         >>> from cool_seq_tool.sources import UtaDatabase
@@ -569,11 +570,17 @@ async def get_mane_c_genomic_data(
             successful
         """
         results = await self.get_tx_exon_aln_v_data(
-            ac, start_pos, end_pos, alt_ac=alt_ac, use_tx_pos=False
+            tx_ac=ac,
+            start_pos=start_pos,
+            end_pos=end_pos,
+            alt_ac=alt_ac,
+            use_tx_pos=False,
         )
         if not results:
             return None
-        result = results[0]
+
+        # Sort by most recent chromosomal accession
+        result = results[-1]
 
         genomic_tx_data = self.data_from_result(result)
         if not genomic_tx_data:

tests/sources/test_uta_database.py

@@ -198,6 +198,33 @@ async def test_mane_c_genomic_data(test_db):
     }
     assert resp == GenomicTxMetadata(**expected_params)
 
+    # Test example where sorting of tx_exon_aln_v is needed
+    resp = await test_db.get_mane_c_genomic_data(
+        "NM_000077.5", "NC_000009.12", 21971186, 21971187
+    )
+    expected_params = {
+        "gene": "CDKN2A",
+        "strand": Strand.NEGATIVE,
+        "tx_pos_range": (180, 487),
+        "alt_pos_range": (21970901, 21971208),
+        "alt_aln_method": "splign",
+        "tx_exon_id": 8314723,
+        "alt_exon_id": 8960507,
+        "coding_start_site": 30,
+        "coding_end_site": 501,
+        "pos_change": (21, 285),
+        "alt_pos_change_range": (21971187, 21971186),
+        "tx_ac": "NM_000077.5",
+        "alt_ac": "NC_000009.12",
+    }
+    assert resp == GenomicTxMetadata(**expected_params)
+
+    # Test case where chromosomal accession is not provided
+    resp = await test_db.get_mane_c_genomic_data(
+        "NM_000077.5", None, 21971186, 21971187
+    )
+    assert resp == GenomicTxMetadata(**expected_params)
+
 
 @pytest.mark.asyncio
 async def test_get_genomic_tx_data(test_db, genomic_tx_data):