Merge branch 'issue-329' into rename-exon-coord

GenomicMedLab · Aug 20, 2024 · e15b490 · e15b490
2 parents 8b56f4e + 88e1c8f
commit e15b490
Showing 1 changed file with 22 additions and 22 deletions.
diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -119,15 +119,15 @@ class _TxSegment(BaseModelForbidExtra):
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
-                "exon_ord": 1,
-                "exon_offset": 0,
+                "exon_ord": 0,
+                "offset": 0,
                 "genomic_location": {
                     "type": "SequenceLocation",
                     "sequenceReference": {
                         "type": "SequenceReference",
-                        "refgetAccession": "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1",
+                        "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                     },
-                    "start": 9575887,
+                    "end": 154192135,
                 },
             }
         }
@@ -159,19 +159,19 @@ def check_errors(cls, values: dict) -> dict:  # noqa: N805
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
-                "gene": "BRAF",
-                "genomic_ac": "NC_000007.14",
-                "tx_ac": "NM_004333.6",
+                "gene": "TPM3",
+                "genomic_ac": "NC_000001.11",
+                "tx_ac": "NM_152263.3",
                 "seg": {
-                    "exon_ord": 5,
-                    "offset": -148,
+                    "exon_ord": 0,
+                    "offset": 0,
                     "genomic_location": {
                         "type": "SequenceLocation",
                         "sequenceReference": {
                             "type": "SequenceReference",
-                            "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                            "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
-                        "end": 140801559,
+                        "end": 154192135,
                     },
                 },
                 "errors": [],
@@ -211,31 +211,31 @@ def add_meta_check_errors(cls, values: dict) -> dict:  # noqa: N805
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
-                "gene": "BRAF",
-                "genomic_ac": "NC_000007.14",
-                "tx_ac": "NM_004333.6",
+                "gene": "TPM3",
+                "genomic_ac": "NC_000001.11",
+                "tx_ac": "NM_152263.3",
                 "seg_start": {
-                    "exon_ord": 5,
-                    "offset": -148,
+                    "exon_ord": 0,
+                    "offset": 0,
                     "genomic_location": {
                         "type": "SequenceLocation",
                         "sequenceReference": {
                             "type": "SequenceReference",
-                            "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                            "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
-                        "end": 140801559,
+                        "end": 154192135,
                     },
                 },
                 "seg_end": {
-                    "exon_ord": 14,
-                    "offset": 57,
+                    "exon_ord": 7,
+                    "offset": 0,
                     "genomic_location": {
                         "type": "SequenceLocation",
                         "sequenceReference": {
                             "type": "SequenceReference",
-                            "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                            "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
-                        "start": 140753336,
+                        "start": 154170399,
                     },
                 },
             }