fix parsing annotations in annotate

Author: Jon Palmer

CITATION.cff

@@ -1,4 +1,4 @@
-cff-version: version = "25.8.3"
+cff-version: version = "25.8.5"
 title: 'funannotate2: eukaryotic genome annotation'
 message: >-
   If you use this software, please cite it using the
@@ -17,5 +17,5 @@ keywords:
   - functional annotation
   - consensus gene models
 license: BSD-2-Clause
-version: version = "25.8.3"
-date-released: '2025-08-04'
+version: version = "25.8.5"
+date-released: '2025-08-05'

funannotate2/annotate.py

@@ -276,7 +276,7 @@ def annotate(args):
         )
         pfam_dict = pfam2tsv(pfam, pfam_all, pfam_annots)
     else:
-        pfam_dict = parse_annotations(pfam_annots)
+        pfam_dict, _ = parse_annotations(pfam_annots)
         logger.info(
             f"Existing Pfam-A results found, loaded annotations for {len(pfam_dict)} gene models"
         )
@@ -296,7 +296,7 @@ def annotate(args):
         )
         dbcan_dict = dbcan2tsv(dbcan, dbcan_all, dbcan_annots)
     else:
-        dbcan_dict = parse_annotations(dbcan_annots)
+        dbcan_dict, _ = parse_annotations(dbcan_annots)
         logger.info(
             f"Existing dbCAN results found, loaded annotations for {len(dbcan_dict)} gene models"
         )
@@ -317,7 +317,7 @@ def annotate(args):
         )
         swiss_dict = swissprot2tsv(swiss, swiss_all, swiss_annots)
     else:
-        swiss_dict = parse_annotations(swiss_annots)
+        swiss_dict, _ = parse_annotations(swiss_annots)
         logger.info(
             f"Existing UniProtKB/Swiss-Prot results found, loaded annotations for {len(swiss_dict)} gene models"
         )
@@ -337,7 +337,7 @@ def annotate(args):
         )
         merops_dict = merops2tsv(merops, merops_all, merops_annots)
     else:
-        merops_dict = parse_annotations(merops_annots)
+        merops_dict, _ = parse_annotations(merops_annots)
         logger.info(
             f"Existing MEROPS results found, loaded annotations for {len(merops_dict)} gene models"
         )
@@ -384,7 +384,7 @@ def annotate(args):
             f"BUSCOlite search resulted in {len(busco_dict)} hits and finished in {round(end - start, 2)} seconds"
         )
     else:
-        busco_dict = parse_annotations(busco_annots)
+        busco_dict, _ = parse_annotations(busco_annots)
         logger.info(
             f"Existing BUSCOlite results found, loaded annotations for {len(busco_dict)} gene models"
         )

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "funannotate2"
-version = "25.8.3"
+version = "25.8.5"
 description = "Funannotate2: eukarytoic genome annotation pipeline"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [