issue #73 - missing gene symbols

Author: davmlaw

generate_transcript_data/gff_parser.py

@@ -108,17 +108,10 @@ def _finish(self):
 
     @staticmethod
     def _create_gene(feature, gene_accession):
-        biotype_set = set()
-        description = None
-
-        # Non mandatory - Ensembl doesn't have some stuff on some RNAs
-        if feature.type in {"gene", "pseudogene", "ncRNA_gene", "mt_gene"}:
-            gene_name = feature.attr.get("Name")
-            description = feature.attr.get("description")
-        else:
-            gene_name = feature.attr.get("gene_name")
+        gene_name = feature.attr.get("gene_name") or feature.attr.get("Name")
+        description = feature.attr.get("description")
 
-        # RefSeq GRCh38 has gene.gene_biotype
+        biotype_set = set()
         biotype = feature.attr.get("gene_biotype") or feature.attr.get("biotype")
         if biotype:
             biotype_set.add(biotype)

generate_transcript_data/json_schema_version.py

@@ -1,3 +1,3 @@
 # After 0.2.22 we split version into separate code (pip) and data schema versions
 # The cdot client will use its own major/minor to determine whether it can read these data files
-JSON_SCHEMA_VERSION = "0.2.24"
+JSON_SCHEMA_VERSION = "0.2.25"