Compute offset using _set_exon_offset, update tests to reflect update…

…d exon_offset
GenomicMedLab · Feb 27, 2024 · fc802d3 · fc802d3
1 parent 4e0208c
commit fc802d3
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Showing 2 changed files with 21 additions and 18 deletions.
diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -571,13 +571,16 @@ async def _genomic_to_transcript_exon_coordinate(
                 params["exon"] = exon
                 params["transcript"] = transcript
                 params["gene"] = gene
-                params["pos"] = (
-                    tx_genomic_coords[exon - 1][3]  # Start genomic coordinate
-                    if is_start
-                    else tx_genomic_coords[exon - 1][4]  # End genomic coordinate
-                )
+                params["pos"] = pos
                 params["chr"] = alt_ac
-                params["exon_offset"] = 0
+                self._set_exon_offset(
+                    params=params,
+                    start=tx_genomic_coords[exon - 1][3],  # Start exon coordinate
+                    end=tx_genomic_coords[exon - 1][4],  # End exon coordinate
+                    pos=pos,
+                    is_start=is_start,
+                    strand=strand,
+                )
                 params["strand"] = strand.value
                 resp.transcript_exon_data = TranscriptExonData(**params)
             return resp

diff --git a/tests/mappers/test_exon_genomic_coords.py b/tests/mappers/test_exon_genomic_coords.py
@@ -195,10 +195,10 @@ def zbtb10_exon3_end():
         "gene": "ZBTB10",
         "chr": "NC_000008.11",
         "start": None,
-        "end": 80514008,
+        "end": 80514009,
         "exon_start": None,
         "exon_end": 3,
-        "exon_end_offset": 0,
+        "exon_end_offset": 100,
         "exon_start_offset": None,
         "transcript": "NM_001105539.3",
         "strand": Strand.POSITIVE,
@@ -212,10 +212,10 @@ def zbtb10_exon5_start():
     params = {
         "gene": "ZBTB10",
         "chr": "NC_000008.11",
-        "start": 80518781,
+        "start": 80518580,
         "end": None,
         "exon_start": 5,
-        "exon_start_offset": 0,
+        "exon_start_offset": -374,
         "exon_end": None,
         "exon_end_offset": None,
         "transcript": "NM_001105539.3",
@@ -231,11 +231,11 @@ def tpm3_exon6_end():
         "gene": "TPM3",
         "chr": "NC_000001.11",
         "start": None,
-        "end": 154171488,
+        "end": 154171409,
         "exon_start": None,
         "exon_start_offset": None,
         "exon_end": 6,
-        "exon_end_offset": 0,
+        "exon_end_offset": 3,
         "transcript": "NM_152263.4",
         "strand": Strand.NEGATIVE,
     }
@@ -248,10 +248,10 @@ def tpm3_exon5_start():
     params = {
         "gene": "TPM3",
         "chr": "NC_000001.11",
-        "start": 154172907,
+        "start": 154173080,
         "end": None,
         "exon_start": 5,
-        "exon_start_offset": 0,
+        "exon_start_offset": -102,
         "exon_end": None,
         "exon_end_offset": None,
         "transcript": "NM_152263.4",
@@ -267,11 +267,11 @@ def gusbp3_exon2_end():
         "gene": "GUSBP3",
         "chr": "NC_000005.10",
         "start": None,
-        "end": 69680799,
+        "end": 69680763,
         "exon_start": None,
         "exon_start_offset": None,
         "exon_end": 2,
-        "exon_end_offset": 0,
+        "exon_end_offset": 2,
         "transcript": "NR_027386.2",
         "strand": Strand.NEGATIVE,
     }
@@ -284,10 +284,10 @@ def gusbp3_exon5_start():
     params = {
         "gene": "GUSBP3",
         "chr": "NC_000005.10",
-        "start": 69642204,
+        "start": 69645878,
         "end": None,
         "exon_start": 5,
-        "exon_start_offset": 0,
+        "exon_start_offset": -3589,
         "exon_end": None,
         "exon_end_offset": None,
         "transcript": "NR_027386.2",