issue #1227 - fix c.HGVS (make it null on any error like VEP now)

SACGF · Jan 17, 2025 · 9a9bfd6 · 9a9bfd6
1 parent 37dbdf8
commit 9a9bfd6
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Showing 3 changed files with 33 additions and 5 deletions.
diff --git a/annotation/management/commands/fix_annotation_sv_c_hgvs.py b/annotation/management/commands/fix_annotation_sv_c_hgvs.py
@@ -4,10 +4,9 @@
 from collections import Counter
 
 from django.core.management.base import BaseCommand
-from django.db.models import Q, Func, Value, F
 
-from annotation.models import VariantAnnotation, VariantTranscriptAnnotation, VariantAnnotationVersion, \
-    TranscriptVersion, defaultdict, AnnotationRun, VariantAnnotationPipelineType, AnnotationStatus
+from annotation.models import VariantAnnotation, VariantTranscriptAnnotation, \
+    TranscriptVersion, AnnotationRun, VariantAnnotationPipelineType, AnnotationStatus
 from genes.hgvs import HGVSMatcher
 from snpdb.models import Variant
 from snpdb.models.models_genome import GenomeBuild
@@ -57,7 +56,7 @@ def handle(self, *args, **options):
                                                                                      transcript_accession)
                             hgvs_c_results["ok"] += 1
                         except Exception as e:
-                            hgvs_c = VariantAnnotation.SV_HGVS_ERROR_MESSAGE
+                            hgvs_c = None  # c.HGVS is ok to be blank
                             hgvs_c_results["error"] += 1
 
                         record.hgvs_c = hgvs_c

diff --git a/annotation/migrations/0123_one_off_fix_annotation_sv_c_hgvs.py b/annotation/migrations/0123_one_off_fix_annotation_sv_c_hgvs.py
@@ -0,0 +1,28 @@
+# Generated by Django 4.2.17 on 2025-01-17 04:00
+
+from django.db import migrations
+
+from manual.operations.manual_operations import ManualOperation
+
+def _check_has_sv_annotation(apps):
+    AnnotationRun = apps.get_model("annotation", "AnnotationRun")
+
+    VAP_STRUCTURAL_VARIANT = 'C'
+    AS_FINISHED = 'F'
+
+    qs = AnnotationRun.objects.filter(pipeline_type=VAP_STRUCTURAL_VARIANT,
+                                      status=AS_FINISHED,
+                                      annotated_count__gt=0)
+    return qs.exists()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotation', '0122_vep_gnomad_t2t'),
+    ]
+
+    operations = [
+        ManualOperation(task_id=ManualOperation.task_id_manage(["fix_annotation_sv_c_hgvs"]),
+                        test=_check_has_sv_annotation)
+    ]
diff --git a/annotation/vcf_files/bulk_vep_vcf_annotation_inserter.py b/annotation/vcf_files/bulk_vep_vcf_annotation_inserter.py
@@ -539,14 +539,15 @@ def _add_hgvs_c(self, variant_coordinate: Optional[VariantCoordinate], transcrip
             return
 
         if transcript_accession:
+
             try:
                 hgvs_c = self.hgvs_matcher.variant_coordinate_to_hgvs_variant(variant_coordinate, transcript_accession)
                 self._generated_hgvs_c["OK"] += 1
                 # TODO: Protein?? hgvs_p
             except Exception as e:
                 logging.error("Error calculating c.HGVS for '%s'/'%s': %s",
                               variant_coordinate, transcript_accession, e)
-                hgvs_c = VariantAnnotation.SV_HGVS_ERROR_MESSAGE
+                hgvs_c = None  # For c.HGVS - it's ok to be blank
                 self._generated_hgvs_c["error"] += 1
 
             transcript_data['hgvs_c'] = hgvs_c