fix backward compatibility issue in GFF3/INSDC

oschwengers · Dec 2, 2024 · 093204d · 093204d
1 parent ff72dda
commit 093204d
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/bakta/io/gff.py b/bakta/io/gff.py
@@ -46,7 +46,7 @@ def write_features(data: dict, features_by_sequence: Dict[str, dict], gff3_path:
             fh.write(f"{seq['id']}\tBakta\tregion\t1\t{str(seq['length'])}\t.\t+\t.\t{annotations}\n")
 
             for feat in features_by_sequence[seq['id']]:
-                seq_id = seq_id if 'sequence' in feat else feat['contig']  # <1.10.0 compatibility
+                seq_id = feat['sequence'] if 'sequence' in feat else feat['contig']  # <1.10.0 compatibility
                 start = feat['start']
                 stop = feat['stop']
                 if('edge' in feat):

diff --git a/bakta/io/insdc.py b/bakta/io/insdc.py
@@ -22,7 +22,9 @@
 def build_biopython_sequence_list(data: dict, features: Sequence[dict]):
     sequence_list = []
     for seq in data['sequences']:
-        sequence_features = [feat for feat in features if feat['sequence'] == seq['id']] if 'sequence' in features[0] else [feat for feat in features if feat['contig'] == seq['id']]  # <1.10.0 compatibility
+        sequence_features = []
+        if len(features) > 0:
+            [feat for feat in features if feat['sequence'] == seq['id']] if 'sequence' in features[0] else [feat for feat in features if feat['contig'] == seq['id']]  # <1.10.0 compatibility
         comment = (
             'Annotated with Bakta',
             f"Software: v{bakta.__version__}\n",