feat: make methods in ManeTranscript public (#326)

close #229

* `ManeTranscript._validate_index` -> `ManeTranscript.validate_index`
* `ManeTranscript._get_reading_frame` -> `ManeTranscript.get_reading_frame`

src/cool_seq_tool/mappers/mane_transcript.py

@@ -128,7 +128,7 @@ def __init__(
         self.liftover = liftover
 
     @staticmethod
-    def _get_reading_frame(pos: int) -> int:
+    def get_reading_frame(pos: int) -> int:
         """Return reading frame number. Only used on c. coordinate.
 
         :param pos: cDNA position
@@ -531,8 +531,8 @@ def _validate_reading_frames(
         """
         for pos, pos_index in [(start_pos, 0), (end_pos, 1)]:
             if pos is not None:
-                og_rf = self._get_reading_frame(pos)
-                new_rf = self._get_reading_frame(transcript_data.pos[pos_index])
+                og_rf = self.get_reading_frame(pos)
+                new_rf = self.get_reading_frame(transcript_data.pos[pos_index])
 
                 if og_rf != new_rf:
                     _logger.warning(
@@ -618,7 +618,7 @@ def _validate_references(
 
         return True
 
-    def _validate_index(
+    def validate_index(
         self, ac: str, pos: tuple[int, int], coding_start_site: int
     ) -> bool:
         """Validate that positions actually exist on accession
@@ -910,7 +910,7 @@ def _get_protein_rep(
                 ac = lcr_result.refseq or lcr_result.ensembl
                 pos = lcr_result.pos
 
-                if not self._validate_index(ac, pos, coding_start_site):
+                if not self.validate_index(ac, pos, coding_start_site):
                     _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
                         pos,
@@ -936,7 +936,7 @@ def _get_protein_rep(
                 cds = lcr_result_dict[k].get("coding_start_site", 0)
                 ac = lcr_result_dict[k]["refseq"] or lcr_result_dict[k]["ensembl"]
                 pos = lcr_result_dict[k]["pos"]
-                if not self._validate_index(ac, pos, cds):
+                if not self.validate_index(ac, pos, cds):
                     valid = False
                     _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
@@ -1114,7 +1114,7 @@ async def g_to_grch38(self, ac: str, start_pos: int, end_pos: int) -> dict | Non
         descr = await self.uta_db.get_chr_assembly(ac)
         if not descr:
             # Already GRCh38 assembly
-            if self._validate_index(ac, (start_pos, end_pos), 0):
+            if self.validate_index(ac, (start_pos, end_pos), 0):
                 return {"ac": ac, "pos": (start_pos, end_pos)}
             return None
         chromosome, assembly = descr
@@ -1145,7 +1145,7 @@ async def g_to_grch38(self, ac: str, start_pos: int, end_pos: int) -> dict | Non
         newest_ac = await self.uta_db.get_newest_assembly_ac(ac)
         if newest_ac:
             ac = newest_ac[0]
-            if self._validate_index(ac, (start_pos, end_pos), 0):
+            if self.validate_index(ac, (start_pos, end_pos), 0):
                 return {"ac": ac, "pos": (start_pos, end_pos)}
         return None
 
@@ -1261,9 +1261,7 @@ async def g_to_mane_c(
                 mane_tx_genomic_data, coding_start_site
             )
 
-            if not self._validate_index(
-                mane_c_ac, mane_c_pos_change, coding_start_site
-            ):
+            if not self.validate_index(mane_c_ac, mane_c_pos_change, coding_start_site):
                 _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,
@@ -1351,9 +1349,7 @@ async def grch38_to_mane_c_p(
             )
 
             # Validate MANE C positions
-            if not self._validate_index(
-                mane_c_ac, mane_c_pos_change, coding_start_site
-            ):
+            if not self.validate_index(mane_c_ac, mane_c_pos_change, coding_start_site):
                 _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,

tests/mappers/test_mane_transcript.py

@@ -177,20 +177,20 @@ def mybpc3_s236g():
 
 
 def test_get_reading_frame(test_mane_transcript):
-    """Test that _get_reading_frame works correctly."""
-    rf = test_mane_transcript._get_reading_frame(1797)
+    """Test that get_reading_frame works correctly."""
+    rf = test_mane_transcript.get_reading_frame(1797)
     assert rf == 3
 
-    rf = test_mane_transcript._get_reading_frame(1798)
+    rf = test_mane_transcript.get_reading_frame(1798)
     assert rf == 1
 
-    rf = test_mane_transcript._get_reading_frame(1799)
+    rf = test_mane_transcript.get_reading_frame(1799)
     assert rf == 2
 
-    rf = test_mane_transcript._get_reading_frame(1800)
+    rf = test_mane_transcript.get_reading_frame(1800)
     assert rf == 3
 
-    rf = test_mane_transcript._get_reading_frame(2573)
+    rf = test_mane_transcript.get_reading_frame(2573)
     assert rf == 2