change 'gene' to 'gene_name' and add 'gene_symbol'

Author: miseminger

bin/gvf2indexandlog.py

@@ -49,7 +49,7 @@ def parse_args():
 
     # create index from GVF
     # make empty index df
-    index_cols=['pos', 'mutation', 'hgvs_aa_mutation', 'hgvs_nt_mutation', 'gene', 'protein_name', 'alias', 'hgvs_alias', 'alias_protein', 'Pokay_annotation', 'lineages']
+    index_cols=['pos', 'mutation', 'hgvs_aa_mutation', 'hgvs_nt_mutation', 'gene_name', 'gene_symbol', 'protein_name', 'protein_symbol', 'alias', 'hgvs_alias', 'alias_protein', 'Pokay_annotation', 'lineages']
     index = pd.DataFrame(np.empty((gvf.shape[0], len(index_cols))), columns=index_cols)
     # populate index df with gvf info
     index['pos'] = gvf['#start']
@@ -60,8 +60,10 @@ def parse_args():
     index['hgvs_alias'] = gvf['hgvs_alias']
     index['alias_protein'] = 'n/a'
     index.loc[index['alias']!='n/a', 'alias_protein'] = gvf['mat_pep']
-    index['gene'] = gvf['gene']
+    index['gene_name'] = gvf['gene_name']
+    index['gene_symbol'] = gvf['gene_symbol']
     index['protein_name'] = gvf['protein_name']
+    index['protein_symbol'] = gvf['protein_symbol']
     index['Pokay_annotation'] = gvf["function_description"].notna()
     index['lineages'] = gvf['viral_lineage']
     # tidying
@@ -73,7 +75,7 @@ def parse_args():
     # create log from index
     log = index.copy()
     # fill in 'new_mutations' column like: "gene:mutation"
-    log['new_mutations'] = log["gene"] + ":" + log["mutation"]
+    log['new_mutations'] = log["gene_symbol"] + ":" + log["mutation"]
     # for orf1ab mutations, fill in 'new_mutations' column like: "gene:mutation / nsp:alias"
     log.loc[log['alias']!='n/a', 'new_mutations'] = log['new_mutations'] + " / " + log["alias_protein"] + ":" + log["alias"]
     # drop duplicates (there shouldn't be any)