Change helper method location and name

Author: jarbesfeld

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -305,22 +305,6 @@ def __init__(
         self.mane_transcript_mappings = mane_transcript_mappings
         self.liftover = liftover
 
-    def _get_mane_status_transcript(self, tx_ac: str) -> TranscriptPriority:
-        """Get MANE status for a transcript
-
-        :param tx_ac: A RefSeq transcript accession
-        :return: A TranscriptPriority object
-        """
-        mane_info = self.mane_transcript_mappings.get_mane_from_transcripts([tx_ac])
-        if not mane_info:
-            return TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
-        mane_info = mane_info[0]["MANE_status"]
-        return (
-            TranscriptPriority.MANE_SELECT
-            if mane_info == "MANE Select"
-            else TranscriptPriority.MANE_PLUS_CLINICAL
-        )
-
     async def tx_segment_to_genomic(
         self,
         transcript: str,
@@ -456,7 +440,7 @@ async def tx_segment_to_genomic(
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
-            tx_status=self._get_mane_status_transcript(transcript),
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg_start=seg_start,
             seg_end=seg_end,
@@ -990,7 +974,7 @@ async def _genomic_to_tx_segment(
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
-            tx_status=self._get_mane_status_transcript(transcript),
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg=TxSegment(
                 exon_ord=exon_num,

src/cool_seq_tool/sources/mane_transcript_mappings.py

@@ -8,7 +8,7 @@
 import polars as pl
 
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
-from cool_seq_tool.schemas import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData, TranscriptPriority
 
 _logger = logging.getLogger(__name__)
 
@@ -85,6 +85,22 @@ def get_mane_from_transcripts(self, transcripts: list[str]) -> list[dict]:
             return []
         return mane_rows.to_dicts()
 
+    def get_transcript_status(self, tx_ac: str) -> TranscriptPriority:
+        """Get MANE status for a transcript
+
+        :param tx_ac: A RefSeq transcript accession
+        :return: A TranscriptPriority object
+        """
+        mane_info = self.get_mane_from_transcripts([tx_ac])
+        if not mane_info:
+            return TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
+        mane_info = mane_info[0]["MANE_status"]
+        return (
+            TranscriptPriority.MANE_SELECT
+            if mane_info == "MANE Select"
+            else TranscriptPriority.MANE_PLUS_CLINICAL
+        )
+
     def get_mane_data_from_chr_pos(
         self, alt_ac: str, start: int, end: int
     ) -> list[dict]:

tests/sources/test_mane_transcript_mappings.py

@@ -5,7 +5,7 @@
 import polars as pl
 import pytest
 
-from cool_seq_tool.schemas import ManeGeneData
+from cool_seq_tool.schemas import ManeGeneData, TranscriptPriority
 
 
 @pytest.fixture(scope="module")
@@ -168,6 +168,15 @@ def test_get_mane_from_transcripts(
     assert resp == []
 
 
+def test_get_transcript_status(test_mane_transcript_mappings):
+    """Test that get_transcript_status works correctly"""
+    actual = test_mane_transcript_mappings.get_transcript_status("NM_152263.4")
+    assert actual == TranscriptPriority.MANE_SELECT
+
+    actual = test_mane_transcript_mappings.get_transcript_status("NM_152263.3")
+    assert actual == TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
+
+
 def test_get_mane_data_from_chr_pos(
     test_mane_transcript_mappings, braf_select, braf_plus_clinical
 ):