From a70608fa2216102e84480e9c5145acb1b23c67bb Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Wed, 13 Nov 2024 13:52:31 +0100 Subject: [PATCH] update CDS Pyrodigal inference tag in GFF3 --- bakta/io/gff.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bakta/io/gff.py b/bakta/io/gff.py index 9834653e..3631cb9b 100644 --- a/bakta/io/gff.py +++ b/bakta/io/gff.py @@ -250,7 +250,7 @@ def write_features(data: dict, features_by_sequence: Dict[str, dict], gff3_path: if(cfg.compliant): gene_id = f"{feat['locus']}_gene" annotations['Parent'] = gene_id - annotations['inference'] = 'EXISTENCE:non-experimental evidence, no additional details recorded' if feat.get('source', None) == bc.CDS_SOURCE_USER else 'ab initio prediction:Prodigal:2.6' + annotations['inference'] = 'EXISTENCE:non-experimental evidence, no additional details recorded' if feat.get('source', None) == bc.CDS_SOURCE_USER else 'ab initio prediction:Pyrodigal:3.5' annotations['Dbxref'], annotations['Note'] = insdc.revise_dbxref_insdc(feat['db_xrefs']) # remove INSDC invalid DbXrefs annotations['Note'], ec_number = insdc.extract_ec_from_notes_insdc(annotations, 'Note') if(ec_number is not None):