Move set_id_prefix to the stable id allocator

src/python/ensembl/io/genomio/gff3/id_allocator.py

@@ -19,7 +19,7 @@
 from dataclasses import dataclass, field
 import logging
 import re
-from typing import List, Set
+from typing import Dict, List, Set
 
 from Bio.SeqFeature import SeqFeature
 
@@ -40,6 +40,16 @@ class StableIDAllocator:
     prefix: str = "TMP_"
     _loaded_ids: Set = field(default_factory=set)
 
+    def set_prefix(self, genome: Dict) -> None:
+        """Sets the ID prefix using the organism abbrev if it exists in the genome metadata."""
+        try:
+            org = genome["BRC4"]["organism_abbrev"]
+        except KeyError:
+            prefix = "TMP_PREFIX_"
+        else:
+            prefix = "TMP_" + org + "_"
+        self.prefix = prefix
+
     def generate_gene_id(self) -> str:
         """Returns a new unique gene stable_id with a prefix.
 

src/python/ensembl/io/genomio/gff3/simplifier.py

@@ -72,30 +72,27 @@ class GFFSimplifier:
     skip_unrecognized = True
     gene_cds_skip_others = False
     allow_pseudogene_with_CDS = False
-    exclude_seq_regions: List = []
-    fail_types: Dict[str, int] = {}
-    stable_ids = StableIDAllocator()
 
     def __init__(self, genome_path: Optional[PathLike] = None):
+        # Load biotypes
         biotypes_json = files(ensembl.io.genomio.data.gff3) / "biotypes.json"
         self._biotypes = get_json(biotypes_json)
-        self.records = Records()
-        self.annotations = FunctionalAnnotations()
+
+        # Load genome metadata
         self.genome = {}
         if genome_path:
             with Path(genome_path).open("r") as genome_fh:
                 self.genome = json.load(genome_fh)
-        self._set_id_prefix()
 
-    def _set_id_prefix(self) -> None:
-        """Sets the ID prefix using the organism abbrev if it exists in the genome metadata."""
-        try:
-            org = self.genome["BRC4"]["organism_abbrev"]
-        except KeyError:
-            prefix = "TMP_PREFIX_"
-        else:
-            prefix = "TMP_" + org + "_"
-        self.stable_ids.prefix = prefix
+        # Other preparations
+        self.stable_ids = StableIDAllocator()
+        self.stable_ids.set_prefix(self.genome)
+        self.exclude_seq_regions: List = []
+        self.fail_types: Dict[str, int] = {}
+
+        # Init the actual data we will store
+        self.records = Records()
+        self.annotations = FunctionalAnnotations()
 
     def simpler_gff3(self, in_gff_path: PathLike) -> None:
         """Loads a GFF3 from INSDC and rewrites it in a simpler version, whilst also writing a

src/python/tests/gff3/test_id_allocator.py

@@ -18,7 +18,7 @@
 from difflib import unified_diff
 import filecmp
 from pathlib import Path
-from typing import ContextManager, List, Optional
+from typing import ContextManager, Dict, List, Optional
 
 import pytest
 
@@ -55,6 +55,20 @@ def _show_diff(result_path: Path, expected_path: Path) -> str:
     return "".join(diff)
 
 
+@pytest.mark.parametrize(
+    "genome, expected_prefix",
+    [
+        pytest.param({}, "TMP_PREFIX_", id="Default prefix"),
+        pytest.param({"BRC4": {"organism_abbrev": "LOREM"}}, "TMP_LOREM_", id="Prefix from genome meta"),
+    ],
+)
+def test_set_prefix(genome: Dict, expected_prefix: str) -> None:
+    """Test prefix setting from genome metadata."""
+    ids = StableIDAllocator()
+    ids.set_prefix(genome)
+    assert ids.prefix == expected_prefix
+
+
 @pytest.mark.parametrize(
     "prefix, expected_ids",
     [