wip: update test examples with @jarbesfeld

cancervariants · Jul 29, 2024 · 0627bb2 · 0627bb2
1 parent 81aaef2
commit 0627bb2
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Showing 4 changed files with 14 additions and 25 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -754,8 +754,7 @@ def exhaustive_example(alk_gene, braf_gene, tpm3_gene):
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         "type": "SequenceReference",
                     },
-                    "start": 154192135,
-                    "end": 154192136,
+                    "end": 154192135,
                 },
                 "elementGenomicEnd": {
                     "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
@@ -770,7 +769,6 @@ def exhaustive_example(alk_gene, braf_gene, tpm3_gene):
                         "type": "SequenceReference",
                     },
                     "start": 154170399,
-                    "end": 154170400,
                 },
             },
             {
@@ -879,8 +877,7 @@ def fusion_example():
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         "type": "SequenceReference",
                     },
-                    "start": 154192135,
-                    "end": 154192136,
+                    "end": 154192135,
                 },
                 "elementGenomicEnd": {
                     "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
@@ -894,8 +891,7 @@ def fusion_example():
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         "type": "SequenceReference",
                     },
-                    "start": 154170399,
-                    "end": 154170400,
+                    "start": 154170399
                 },
             },
             {

diff --git a/tests/test_fusor.py b/tests/test_fusor.py
@@ -194,27 +194,25 @@ def transcript_segment_element():
             "type": "Gene",
         },
         "transcript": "refseq:NM_152263.3",
-        "elementGenomicEnd": {
-            "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
+        "elementGenomicStart": {
+            "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
             "type": "SequenceLocation",
             "sequenceReference": {
                 "id": "refseq:NC_000001.11",
                 "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 "type": "SequenceReference",
             },
-            "start": 154170399,
-            "end": 154170400,
+            "end": 154192135
         },
-        "elementGenomicStart": {
-            "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO",
+        "elementGenomicEnd": {
+            "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
             "type": "SequenceLocation",
             "sequenceReference": {
                 "id": "refseq:NC_000001.11",
                 "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 "type": "SequenceReference",
             },
-            "start": 154192135,
-            "end": 154192136,
+            "start": 154170399
         },
     }
     return TranscriptSegmentElement(**params)
@@ -245,7 +243,6 @@ def mane_transcript_segment_element():
                 "type": "SequenceReference",
             },
             "start": 9575887,
-            "end": 9575886,
         },
     }
     return TranscriptSegmentElement(**params)

diff --git a/tests/test_models.py b/tests/test_models.py
@@ -178,7 +178,7 @@ def transcript_segments(sequence_locations, gene_examples):
         },
         {
             "type": "TranscriptSegmentElement",
-            "transcript": "refseq:NM_034348.3",
+            "transcript": "refseq:NM_034348.3",  # DNE
             "exonStart": 1,
             "exonEnd": 8,
             "gene": gene_examples[3],
@@ -187,7 +187,7 @@ def transcript_segments(sequence_locations, gene_examples):
         },
         {
             "type": "TranscriptSegmentElement",
-            "transcript": "refseq:NM_938439.4",
+            "transcript": "refseq:NM_938439.4",  # DNE
             "exonStart": 7,
             "exonEnd": 14,
             "exonEndOffset": -5,
@@ -197,7 +197,7 @@ def transcript_segments(sequence_locations, gene_examples):
         },
         {
             "type": "TranscriptSegmentElement",
-            "transcript": "refseq:NM_938439.4",
+            "transcript": "refseq:NM_938439.4",  # DNE
             "exonStart": 7,
             "gene": gene_examples[4],
             "elementGenomicStart": sequence_locations[0],

diff --git a/tests/test_nomenclature.py b/tests/test_nomenclature.py
@@ -127,8 +127,7 @@ def exon_offset_example():
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         "type": "SequenceReference",
                     },
-                    "start": 156864428,
-                    "end": 156864429,
+                    "start": 156864353
                 },
             },
         ],
@@ -154,8 +153,7 @@ def tx_seg_example():
                 "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                 "type": "SequenceReference",
             },
-            "start": 154192135,
-            "end": 154192136,
+            "end": 154192135,
         },
         elementGenomicEnd={
             "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi",
@@ -166,7 +164,6 @@ def tx_seg_example():
                 "type": "SequenceReference",
             },
             "start": 154170399,
-            "end": 154170400,
         },
     )
 
@@ -193,7 +190,6 @@ def junction_example():
                 "type": "SequenceReference",
             },
             "start": 154170399,
-            "end": 154170400,
         },
     )