fix GFF3 INSDC output

oschwengers · Nov 13, 2024 · 89178f4 · 89178f4
1 parent 7b53962
commit 89178f4
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/bakta/io/gff.py b/bakta/io/gff.py
@@ -169,7 +169,7 @@ def write_features(data: dict, features_by_sequence: Dict[str, dict], gff3_path:
                         if(ba.RE_GENE_SYMBOL.fullmatch(feat['gene'])):  # discard non-standard ncRNA gene symbols
                             gene_annotations['gene'] = feat['gene']
                         else:
-                            annotations.pop('gene')
+                            annotations.pop('gene', None)
                         if('truncated' in feat):
                             gene_annotations[bc.INSDC_FEATURE_PSEUDO] = True
                         gene_annotations = encode_annotations(gene_annotations)

diff --git a/bakta/io/insdc.py b/bakta/io/insdc.py
@@ -263,7 +263,7 @@ def build_biopython_sequence_list(data: dict, features: Sequence[dict]):
                         if(ba.RE_GENE_SYMBOL.fullmatch(feature['gene'])):  # discard non-standard gene symbols
                             gene_qualifier['gene'] = feature['gene']
                         else:
-                            qualifiers.pop('gene')
+                            qualifiers.pop('gene', None)
                     else:
                         qualifiers['gene'] = feature['gene']
                         gene_qualifier['gene'] = feature['gene']