update

src/cool_seq_tool/mappers/mane_transcript.py

@@ -25,12 +25,12 @@
 from cool_seq_tool.schemas import (
     AnnotationLayer,
     Assembly,
+    ManeGeneData,
     ResidueMode,
     Strand,
     TranscriptPriority,
 )
 from cool_seq_tool.sources import (
-    ManeGeneData,
     ManeTranscriptMappings,
     TranscriptMappings,
     UtaDatabase,

src/cool_seq_tool/schemas.py

@@ -116,6 +116,14 @@ class BaseModelForbidExtra(BaseModel, extra="forbid"):
     """Base Pydantic model class with extra values forbidden."""
 
 
+class ManeGeneData(BaseModel, extra="forbid"):
+    """Define minimal object model for representing a MANE gene"""
+
+    ncbi_gene_id: StrictInt
+    hgnc_id: StrictInt | None
+    symbol: StrictStr
+
+
 class TranscriptExonData(BaseModelForbidExtra):
     """Model containing transcript exon data."""
 

src/cool_seq_tool/sources/__init__.py

@@ -1,11 +1,10 @@
 """Module for providing basic acquisition/setup for the various resources"""
 
-from .mane_transcript_mappings import ManeGeneData, ManeTranscriptMappings
+from .mane_transcript_mappings import ManeTranscriptMappings
 from .transcript_mappings import TranscriptMappings
 from .uta_database import UtaDatabase
 
 __all__ = [
-    "ManeGeneData",
     "ManeTranscriptMappings",
     "TranscriptMappings",
     "UtaDatabase",

src/cool_seq_tool/sources/mane_transcript_mappings.py

@@ -6,21 +6,13 @@
 from pathlib import Path
 
 import polars as pl
-from pydantic import BaseModel, StrictInt, StrictStr
 
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
+from cool_seq_tool.schemas import ManeGeneData
 
 _logger = logging.getLogger(__name__)
 
 
-class ManeGeneData(BaseModel, extra="forbid"):
-    """Define minimal object model for representing a MANE gene"""
-
-    ncbi_gene_id: StrictInt
-    hgnc_id: StrictInt | None
-    symbol: StrictStr
-
-
 class ManeTranscriptMappings:
     """Provide fast tabular access to MANE summary file.
 

tests/conftest.py

@@ -5,8 +5,7 @@
 import pytest
 
 from cool_seq_tool.app import CoolSeqTool
-from cool_seq_tool.schemas import Strand
-from cool_seq_tool.sources import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData, Strand
 
 
 @pytest.fixture(scope="session")

tests/mappers/test_mane_transcript.py

@@ -671,19 +671,36 @@ async def test_get_longest_compatible_transcript(test_mane_transcript):
 @pytest.mark.asyncio()
 async def test_g_to_grch38(test_mane_transcript, grch38_egfr, grch38_braf):
     """Test that g_to_grch38 method works correctly."""
-    resp = await test_mane_transcript.g_to_grch38("NC_000007.13", 55259515, 55259515)
+    resp = await test_mane_transcript.g_to_grch38(
+        "NC_000007.13", 55259515, 55259515, get_mane_genes=False
+    )
+    grch38_egfr_no_genes = grch38_egfr.copy()
+    grch38_egfr_no_genes.mane_genes = []
+    assert resp == grch38_egfr_no_genes
+
+    resp = await test_mane_transcript.g_to_grch38(
+        "NC_000007.13", 55259515, 55259515, get_mane_genes=True
+    )
     assert resp == grch38_egfr
 
-    resp = await test_mane_transcript.g_to_grch38("NC_000007.13", 140453136, 140453136)
+    resp = await test_mane_transcript.g_to_grch38(
+        "NC_000007.13", 140453136, 140453136, get_mane_genes=True
+    )
     assert resp == grch38_braf
 
     resp = await test_mane_transcript.g_to_grch38(
-        "NC_000007.13", 140453135, 140453136, residue_mode=ResidueMode.INTER_RESIDUE
+        "NC_000007.13",
+        140453135,
+        140453136,
+        residue_mode=ResidueMode.INTER_RESIDUE,
+        get_mane_genes=True,
     )
     assert resp == grch38_braf
 
     # Already on GRCh38
-    resp = await test_mane_transcript.g_to_grch38("NC_000007.14", 140753336, 140753336)
+    resp = await test_mane_transcript.g_to_grch38(
+        "NC_000007.14", 140753336, 140753336, get_mane_genes=True
+    )
     assert resp == grch38_braf
 
 

tests/sources/test_mane_transcript_mappings.py

@@ -5,7 +5,7 @@
 import polars as pl
 import pytest
 
-from cool_seq_tool.sources import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData
 
 
 @pytest.fixture(scope="module")