update transcript segment element location

cancervariants · Aug 22, 2024 · 29ecc8c · 29ecc8c
1 parent 6c5c8a3
commit 29ecc8c
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Showing 3 changed files with 24 additions and 20 deletions.
diff --git a/src/fusor/models.py b/src/fusor/models.py
@@ -170,26 +170,26 @@ def check_exons(cls, values):
                     "label": "TPM3",
                 },
                 "elementGenomicStart": {
-                    "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+                    "id": "ga4gh:SL.Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
+                    "digest": "Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
                     "type": "SequenceLocation",
                     "sequenceReference": {
                         "id": "refseq:NC_000001.11",
                         "type": "SequenceReference",
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                     },
-                    "start": 154192135,
-                    "end": 154192136,
+                    "end": 154192135,
                 },
                 "elementGenomicEnd": {
-                    "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+                    "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
+                    "digest": "Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
                     "type": "SequenceLocation",
                     "sequenceReference": {
                         "id": "refseq:NC_000001.11",
                         "type": "SequenceReference",
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                     },
                     "start": 154170399,
-                    "end": 154170400,
                 },
             }
         },
@@ -703,26 +703,26 @@ class CategoricalFusion(AbstractFusion):
                             "label": "TPM3",
                         },
                         "elementGenomicStart": {
-                            "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+                            "id": "ga4gh:SL.Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
+                            "digest": "Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
                             "type": "SequenceLocation",
                             "sequenceReference": {
                                 "id": "refseq:NC_000001.11",
-                                "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                                 "type": "SequenceReference",
+                                "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                             },
-                            "start": 154192135,
-                            "end": 154192136,
+                            "end": 154192135,
                         },
                         "elementGenomicEnd": {
-                            "id": "ga4gh:SL.m5_Spfzt1v4sfVw9u4kmuYn7dM7gyNeb",
+                            "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
+                            "digest": "Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
                             "type": "SequenceLocation",
                             "sequenceReference": {
                                 "id": "refseq:NC_000001.11",
-                                "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                                 "type": "SequenceReference",
+                                "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                             },
-                            "start": 154170398,
-                            "end": 154170399,
+                            "start": 154170399,
                         },
                     },
                     {

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -743,7 +743,8 @@ def exhaustive_example(alk_gene, braf_gene, tpm3_gene):
                 "exonEndOffset": 0,
                 "gene": tpm3_gene,
                 "elementGenomicStart": {
-                    "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+                    "id": "ga4gh:SL.Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
+                    "digest": "Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
                     "description": None,
                     "xrefs": None,
                     "alternativeLabels": None,
@@ -757,7 +758,8 @@ def exhaustive_example(alk_gene, braf_gene, tpm3_gene):
                     "end": 154192135,
                 },
                 "elementGenomicEnd": {
-                    "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+                    "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
+                    "digest": "Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
                     "description": None,
                     "xrefs": None,
                     "alternativeLabels": None,
@@ -866,7 +868,8 @@ def fusion_example():
                     "id": "hgnc:12012",
                 },
                 "elementGenomicStart": {
-                    "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+                    "id": "ga4gh:SL.Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
+                    "digest": "Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
                     "description": None,
                     "xrefs": None,
                     "alternativeLabels": None,
@@ -880,7 +883,8 @@ def fusion_example():
                     "end": 154192135,
                 },
                 "elementGenomicEnd": {
-                    "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+                    "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
+                    "digest": "Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
                     "description": None,
                     "xrefs": None,
                     "alternativeLabels": None,

diff --git a/tests/test_nomenclature.py b/tests/test_nomenclature.py
@@ -146,7 +146,7 @@ def tx_seg_example():
         exonEndOffset=0,
         gene=Gene(id="hgnc:12012", label="TPM3"),
         elementGenomicStart={
-            "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+            "id": "ga4gh:SL.Q8vkGp7_xR9vI0PQ7g1IvUUeQ4JlJG8l",
             "type": "SequenceLocation",
             "sequenceReference": {
                 "id": "refseq:NC_000001.11",
@@ -156,7 +156,7 @@ def tx_seg_example():
             "end": 154192135,
         },
         elementGenomicEnd={
-            "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+            "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
             "type": "SequenceLocation",
             "sequenceReference": {
                 "id": "refseq:NC_000001.11",
@@ -182,7 +182,7 @@ def junction_example():
             "id": "hgnc:12012",
         },
         elementGenomicEnd={
-            "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+            "id": "ga4gh:SL.Lnne0bSsgjzmNkKsNnXg98FeJSrDJuLb",
             "type": "SequenceLocation",
             "sequenceReference": {
                 "id": "refseq:NC_000001.11",