feat!: Use longest compatible remaining transcript (#439)

closes #438

Author: jarbesfeld

src/cool_seq_tool/app.py

@@ -107,6 +107,7 @@ def __init__(
         self.ex_g_coords_mapper = ExonGenomicCoordsMapper(
             self.seqrepo_access,
             self.uta_db,
+            self.mane_transcript,
             self.mane_transcript_mappings,
             self.liftover,
         )

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -8,7 +8,9 @@
 
 from cool_seq_tool.handlers.seqrepo_access import SeqRepoAccess
 from cool_seq_tool.mappers.liftover import LiftOver
+from cool_seq_tool.mappers.mane_transcript import ManeTranscript
 from cool_seq_tool.schemas import (
+    AnnotationLayer,
     Assembly,
     BaseModelForbidExtra,
     CoordinateType,
@@ -273,6 +275,7 @@ def __init__(
         self,
         seqrepo_access: SeqRepoAccess,
         uta_db: UtaDatabase,
+        mane_transcript: ManeTranscript,
         mane_transcript_mappings: ManeTranscriptMappings,
         liftover: LiftOver,
     ) -> None:
@@ -297,11 +300,13 @@ def __init__(
 
         :param seqrepo_access: SeqRepo instance to give access to query SeqRepo database
         :param uta_db: UtaDatabase instance to give access to query UTA database
+        :param mane_transcript: ManeTranscript instance to give access to ManeTranscript class
         :param mane_transcript_mappings: Instance to provide access to ManeTranscriptMappings class
         :param liftover: Instance to provide mapping between human genome assemblies
         """
         self.seqrepo_access = seqrepo_access
         self.uta_db = uta_db
+        self.mane_transcript = mane_transcript
         self.mane_transcript_mappings = mane_transcript_mappings
         self.liftover = liftover
 
@@ -870,14 +875,18 @@ async def _genomic_to_tx_segment(
             if mane_transcripts:
                 transcript = mane_transcripts[0]["RefSeq_nuc"]
             else:
-                # Attempt to find a coding transcript if a MANE transcript
+                # Attempt to find longest compatible transcript if a MANE transcript
                 # cannot be found
-                results = await self.uta_db.get_transcripts(
-                    gene=gene, alt_ac=genomic_ac
+                results = await self.mane_transcript.get_longest_compatible_transcript(
+                    start_pos=genomic_pos,
+                    end_pos=genomic_pos,
+                    gene=gene,
+                    alt_ac=genomic_ac,
+                    start_annotation_layer=AnnotationLayer.GENOMIC,
                 )
 
-                if not results.is_empty():
-                    transcript = results[0]["tx_ac"][0]
+                if results:
+                    transcript = results.refseq
                 else:
                     # Run if gene is for a noncoding transcript
                     query = f"""

tests/mappers/test_exon_genomic_coords.py

@@ -1071,6 +1071,17 @@ async def test_genomic_to_transcript_fusion_context(
     resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     genomic_tx_seg_service_checks(resp, gusbp3_exon5_start)
 
+    # Test case where gene does not have a MANE transcript. We are looking
+    # to check that the same transcript accession is returned across runs
+    inputs = {
+        "genomic_ac": "NC_000001.11",
+        "seg_end_genomic": 156421555,
+        "gene": "MIR9-1HG",
+    }
+    resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
+    assert resp.tx_ac == "NM_001320454.2"
+    assert resp.tx_status == "longest_compatible_remaining"
+
 
 @pytest.mark.asyncio
 async def test_get_alt_ac_start_and_end(