add override for --augustus-species and --busco-lineage to train; #13

Author: Jon Palmer

CITATION.cff

@@ -1,4 +1,4 @@
-cff-version: version = "25.6.20"
+cff-version: version = "25.6.22"
 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 = "25.6.20"
-date-released: '2025-06-20'
+version: version = "25.6.22"
+date-released: '2025-06-22'

funannotate2/__main__.py

@@ -338,6 +338,18 @@ def train_subparser(subparsers):
         help="Max length for fasta headers",
         metavar="",
     )
+    optional_args.add_argument(
+        "--busco-lineage",
+        dest="busco_lineage",
+        help="BUSCO lineage to use, over-rides default auto selection",
+        metavar="",
+    )
+    optional_args.add_argument(
+        "--augustus-species",
+        dest="augustus_species",
+        help="Pre-trained augustus species to use as initial parameters for BUSCO, over-rides default auto selection",
+        metavar="",
+    )
     other_args = group.add_argument_group("Other arguments")
     other_args.add_argument(
         "-h",

funannotate2/config.py

@@ -184,15 +184,6 @@
         "genus": "Brugia",
         "species": "Brugia malayi",
     },
-    "b_pseudomallei": {
-        "superkingdom": "Bacteria",
-        "phylum": "Pseudomonadota",
-        "class": "Betaproteobacteria",
-        "order": "Burkholderiales",
-        "family": "Burkholderiaceae",
-        "genus": "Burkholderia",
-        "species": "Burkholderia pseudomallei",
-    },
     "caenorhabditis": {
         "superkingdom": "Eukaryota",
         "kingdom": "Metazoa",
@@ -468,15 +459,6 @@
         "genus": "Eremothecium",
         "species": "Eremothecium gossypii",
     },
-    "E_coli_K12": {
-        "superkingdom": "Bacteria",
-        "phylum": "Pseudomonadota",
-        "class": "Gammaproteobacteria",
-        "order": "Enterobacterales",
-        "family": "Enterobacteriaceae",
-        "genus": "Escherichia",
-        "species": "Escherichia coli",
-    },
     "fusarium_graminearum": {
         "superkingdom": "Eukaryota",
         "kingdom": "Fungi",
@@ -868,24 +850,6 @@
         "genus": "Solanum",
         "species": "Solanum lycopersicum",
     },
-    "s_aureus": {
-        "superkingdom": "Bacteria",
-        "phylum": "Bacillota",
-        "class": "Bacilli",
-        "order": "Bacillales",
-        "family": "Staphylococcaceae",
-        "genus": "Staphylococcus",
-        "species": "Staphylococcus aureus",
-    },
-    "s_pneumoniae": {
-        "superkingdom": "Bacteria",
-        "phylum": "Bacillota",
-        "class": "Bacilli",
-        "order": "Lactobacillales",
-        "family": "Streptococcaceae",
-        "genus": "Streptococcus",
-        "species": "Streptococcus pneumoniae",
-    },
     "strongylocentrotus_purpuratus": {
         "superkingdom": "Eukaryota",
         "kingdom": "Metazoa",
@@ -896,14 +860,6 @@
         "genus": "Strongylocentrotus",
         "species": "Strongylocentrotus purpuratus",
     },
-    "sulfolobus_solfataricus": {
-        "superkingdom": "Archaea",
-        "phylum": "Thermoproteota",
-        "class": "Thermoprotei",
-        "order": "Sulfolobales",
-        "family": "Sulfolobaceae",
-        "genus": "Sulfolobus",
-    },
     "tetrahymena": {
         "superkingdom": "Eukaryota",
         "phylum": "Ciliophora",
@@ -923,14 +879,6 @@
         "genus": "Theobroma",
         "species": "Theobroma cacao",
     },
-    "thermoanaerobacter_tengcongensis": {
-        "superkingdom": "Bacteria",
-        "phylum": "Bacillota",
-        "class": "Clostridia",
-        "order": "Thermoanaerobacterales",
-        "family": "Thermoanaerobacteraceae",
-        "genus": "Thermoanaerobacter",
-    },
     "toxoplasma": {
         "superkingdom": "Eukaryota",
         "phylum": "Apicomplexa",

funannotate2/train.py

@@ -33,6 +33,33 @@
     get_odb_version,
     rename_gff_contigs,
 )
+from .config import augustus_species, busco_taxonomy
+
+
+def validate_augustus_species(species_name):
+    """
+    Validate that the provided Augustus species is available in the config.
+
+    Parameters:
+    - species_name (str): The Augustus species name to validate
+
+    Returns:
+    - bool: True if valid, False otherwise
+    """
+    return species_name in augustus_species
+
+
+def validate_busco_lineage(lineage_name):
+    """
+    Validate that the provided BUSCO lineage is available in the config.
+
+    Parameters:
+    - lineage_name (str): The BUSCO lineage name to validate
+
+    Returns:
+    - bool: True if valid, False otherwise
+    """
+    return lineage_name in busco_taxonomy
 
 
 def train(args):
@@ -93,12 +120,34 @@ def train(args):
     taxonomy = lookup_taxonomy(args.species)
     logger.info(f"Getting taxonomy information\n{json.dumps(taxonomy, indent=2)}")
 
-    # choose best augustus species based on taxonomy
-    aug_species = choose_best_augustus_species(taxonomy)
-    logger.info(f"Choosing best augustus species based on taxonomy: {aug_species}")
-
-    # choose best busco species
-    busco_species = choose_best_busco_species(taxonomy)
+    # validate and set augustus species
+    if args.augustus_species:
+        if not validate_augustus_species(args.augustus_species):
+            logger.critical(f"Invalid Augustus species: {args.augustus_species}")
+            logger.critical(
+                f"Valid options are: {', '.join(sorted(augustus_species.keys()))}"
+            )
+            raise SystemExit(1)
+        aug_species = args.augustus_species
+        logger.info(f"Using user-specified Augustus species: {aug_species}")
+    else:
+        # choose best augustus species based on taxonomy
+        aug_species = choose_best_augustus_species(taxonomy)
+        logger.info(f"Choosing best augustus species based on taxonomy: {aug_species}")
+
+    # validate and set busco lineage
+    if args.busco_lineage:
+        if not validate_busco_lineage(args.busco_lineage):
+            logger.critical(f"Invalid BUSCO lineage: {args.busco_lineage}")
+            logger.critical(
+                f"Valid options are: {', '.join(sorted(busco_taxonomy.keys()))}"
+            )
+            raise SystemExit(1)
+        busco_species = args.busco_lineage
+        logger.info(f"Using user-specified BUSCO lineage: {busco_species}")
+    else:
+        # choose best busco species
+        busco_species = choose_best_busco_species(taxonomy)
     # pull the latest odb version from downloads link
     odb_version = get_odb_version(
         os.path.join(os.path.dirname(__file__), "downloads.json")

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "funannotate2"
-version = "25.6.20"
+version = "25.6.22"
 description = "Funannotate2: eukarytoic genome annotation pipeline"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [