da2a89e8c4b23469cb35ec86b066bca2c4504745
lrnassar
  Wed Aug 7 15:39:34 2024 -0700
Adding a new check to panelApp otto that started failing, before all panelApp genes had an OMIM ID associated with it, so that field of the JSON file was a list with (usually) just one OMIM ID. But now there is a single gene with no associated ID so it returns None instead of a list. No RM.

diff --git src/hg/utils/otto/panelApp/tandRep.py src/hg/utils/otto/panelApp/tandRep.py
index a38fa9f..b51584f 100644
--- src/hg/utils/otto/panelApp/tandRep.py
+++ src/hg/utils/otto/panelApp/tandRep.py
@@ -59,30 +59,33 @@
         entity_type = res[count]['entity_type']
         evidence = ' '.join(res[count]['evidence'])
         
         gene_data = res[count]['gene_data']
         alias = ' '.join(gene_data['alias'])
         biotype = gene_data['biotype']
         ensembl_id_37 = gene_data['ensembl_genes']['GRch37']['82']['ensembl_id']
         #ensembl_location_37 = gene_data['ensembl_genes']['GRch37']['82']['location']
         ensembl_id_38 = gene_data['ensembl_genes']['GRch38']['90']['ensembl_id']
         #ensembl_location_38 = gene_data['ensembl_genes']['GRch38']['90']['location']
         gene_name = gene_data['gene_name']
         #gene_symbol = gene_data['gene_symbol']
         #hgnc_date_symbol_changed = gene_data['hgnc_date_symbol_changed']
         hgnc_id = gene_data['hgnc_id']
         hgnc_symbol = gene_data['hgnc_symbol']
+        if str(gene_data['omim_gene']) == "None":
+            omim_gene = "None"
+        else:
             omim_gene = ' '.join(gene_data['omim_gene'])
         grch37_coordinates = res[count]['grch37_coordinates']
         if grch37_coordinates == None:
             coordinates = gene_data['ensembl_genes']['GRch37']['82']['location'] 
             location = coordinates.split(':')
             grch37_coordinates = location[1].split('-')
         chromStart_19 = int(grch37_coordinates[0])
         chromEnd_19 = int(grch37_coordinates[1])
 
         # hg38
         grch38_coordinates = res[count]['grch38_coordinates']
         if grch38_coordinates == None:
             coordinates = gene_data['ensembl_genes']['GRch38']['90']['location'] 
             location = coordinates.split(':')
             grch38_coordinates = location[1].split('-')