Do not require gene when using get_nearest_transcript_junction

GenomicMedLab · Sep 25, 2024 · 293ac12 · 293ac12
1 parent 0f7fc9a
commit 293ac12
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -770,10 +770,10 @@ async def _genomic_to_tx_segment(
         params = {key: None for key in GenomicTxSeg.model_fields}
 
         if get_nearest_transcript_junction:
-            if not gene:
+            if not gene and not transcript:
                 return GenomicTxSeg(
                     errors=[
-                        "`gene` must be provided to select the adjacent transcript junction"
+                        "`gene` or `transcript` must be provided to select the adjacent transcript junction"
                     ]
                 )
 

diff --git a/tests/mappers/test_exon_genomic_coords.py b/tests/mappers/test_exon_genomic_coords.py
@@ -928,16 +928,15 @@ 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)
 
-    inputs = {  # Test when gene and strand are not provided
+    inputs = {  # Test when gene and transcript are not provided
         "chromosome": "5",
         "seg_start_genomic": 69645878,
-        "transcript": "NR_027386.2",
         "get_nearest_transcript_junction": True,
     }
     resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     assert (
         resp.errors[0]
-        == "`gene` must be provided to select the adjacent transcript junction"
+        == "`gene` or `transcipt` must be provided to select the adjacent transcript junction"
     )
 
     inputs = {  # Test when transcript is provided
@@ -950,6 +949,15 @@ 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)
 
+    inputs = {  # Test when gene is not provided
+        "genomic_ac": "NC_000005.10",
+        "seg_start_genomic": 69645878,
+        "transcript": "NR_027386.2",
+        "get_nearest_transcript_junction": True,
+    }
+    resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
+    genomic_tx_seg_service_checks(resp, gusbp3_exon5_start)
+
 
 @pytest.mark.asyncio()
 async def test_get_alt_ac_start_and_end(