missing get_anno_db fixed

pombase · Aug 30, 2023 · 75d76e4 · 75d76e4
1 parent e8081e2
commit 75d76e4
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/protein_modification_transvar.py b/protein_modification_transvar.py
@@ -71,7 +71,7 @@ def main(genome_file, protein_modification_results_file, exclude_transcripts_fil
     # Apply transvar syntax to each sequence position
     data_exploded['transvar_input'] = data_exploded.apply(format_for_transvar, axis=1, args=(genome,))
 
-    anno_db = get_anno_db()
+    anno_db = get_anno_db('data/pombe_genome.gtf.transvardb', 'data/pombe_genome.fa')
     print('Running transvar on protein modifications... (will take a while)')
     data_exploded['transvar_coordinates'] = data_exploded.progress_apply(get_transvar_coordinates, args=(anno_db, genome, exclude_transcripts), axis=1)