fixed a bug in consequence annotation

GC-HBOC · Jun 3, 2024 · a449d3f · a449d3f
1 parent 790ce6d
commit a449d3f
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/src/annotation_service/annotation_jobs/consequence_job.py b/src/annotation_service/annotation_jobs/consequence_job.py
@@ -51,12 +51,14 @@ def save_to_db(self, info, variant_id, conn):
         # T|upstream_gene_variant|MODIFIER|FTLP14|HGNC:37964|ENST00000562087.2|Transcript||||,
         # T|upstream_gene_variant|MODIFIER|CDH1|HGNC:1748|ENST00000562118.1|Transcript||||
         for source in sources:
-            info_field = info_field_prefix + source
+            info_field = info_field_prefix + source + "="
             csq_info = functions.find_between(info, info_field, '(;|$)')
             if csq_info is None:
                 continue
             csq_entries = csq_info.split(',')
             for csq_entry in csq_entries:
+                if csq_entry.strip() == '':
+                    continue
                 parts = csq_entry.strip().split('|')
                 feature_type = parts[6]
                 if feature_type.lower() != "transcript":