add peptide tag info to tmRNA feature

oschwengers · Oct 7, 2024 · 011bb1a · 011bb1a
1 parent 0f14902
commit 011bb1a
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diff --git a/bakta/features/tm_rna.py b/bakta/features/tm_rna.py
@@ -72,6 +72,7 @@ def predict_tm_rnas(genome: dict, contigs_path: Path):
                     tmrna['strand'] = strand
                     tmrna['gene'] = 'ssrA'
                     tmrna['product'] = 'transfer-messenger RNA, SsrA'
+                    tmrna['tag_aa'] = tag_aa.replace('*', '')
                     tmrna['db_xrefs'] = [so.SO_TMRNA.id]
 
                     nt = bu.extract_feature_sequence(tmrna, contigs[contig_id])  # extract nt sequences

diff --git a/bakta/io/gff.py b/bakta/io/gff.py
@@ -91,6 +91,7 @@ def write_gff3(genome: dict, features_by_contig: Dict[str, dict], gff3_path: Pat
                         'locus_tag': feat['locus'],
                         'gene': feat['gene'],
                         'product': feat['product'],
+                        'tag_peptide': feat['tag_aa'],
                         'Dbxref': feat['db_xrefs']
                     }
                     if(cfg.compliant):

diff --git a/bakta/io/insdc.py b/bakta/io/insdc.py
@@ -189,6 +189,7 @@ def write_insdc(genome: dict, features: Sequence[dict], genbank_output_path: Pat
                     qualifiers['pseudo'] = None
             elif(feature['type'] == bc.FEATURE_TM_RNA):
                 qualifiers['inference'] = 'profile:aragorn:1.2'
+                qualifiers['tag_peptide'] = feature['tag_aa']
                 insdc_feature_type = bc.INSDC_FEATURE_TM_RNA
             elif(feature['type'] == bc.FEATURE_R_RNA):
                 for rfam_id in [dbxref.split(':')[1] for dbxref in feature['db_xrefs'] if dbxref.split(':')[0] == bc.DB_XREF_RFAM]: