From 589a6b1ddf0d63f3901b661b59f2fb7de883ad43 Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Tue, 26 Dec 2023 08:50:49 -0500
Subject: [PATCH] rm zero based

---
 cool_seq_tool/mappers/mane_transcript.py | 10 +++++-----
 cool_seq_tool/schemas.py                 |  1 -
 cool_seq_tool/utils.py                   |  2 --
 tests/test_utils.py                      |  4 ----
 4 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/cool_seq_tool/mappers/mane_transcript.py b/cool_seq_tool/mappers/mane_transcript.py
index ea7aad27..6a362062 100644
--- a/cool_seq_tool/mappers/mane_transcript.py
+++ b/cool_seq_tool/mappers/mane_transcript.py
@@ -174,7 +174,9 @@ async def _c_to_g(self, ac: str, pos: Tuple[int, int]) -> Optional[Dict]:
             if not self.transcript_mappings.ensembl_transcript_version_to_gene_symbol.get(
                 ac
             ):
-                if not self.seqrepo_access.get_reference_sequence(ac, start=1, end=1)[0]:
+                if not self.seqrepo_access.get_reference_sequence(ac, start=1, end=1)[
+                    0
+                ]:
                     logger.warning(f"Ensembl transcript not found: {ac}")
                     return None
 
@@ -508,9 +510,7 @@ def _validate_index(
         end_pos = pos[1] + coding_start_site
         if self.seqrepo_access.get_reference_sequence(
             ac, start=start_pos, end=end_pos, residue_mode=ResidueMode.INTER_RESIDUE
-        )[
-            0
-        ]:
+        )[0]:
             return True
         else:
             return False
@@ -808,7 +808,7 @@ async def get_mane_transcript(
         gene: Optional[str] = None,
         ref: Optional[str] = None,
         try_longest_compatible: bool = False,
-        residue_mode: Union[ResidueMode.RESIDUE, ResidueMode.INTER_RESIDUE] = ResidueMode.RESIDUE,
+        residue_mode: ResidueMode = ResidueMode.RESIDUE,
     ) -> Optional[Union[DataRepresentation, CdnaRepresentation]]:
         """Return mane transcript.
 
diff --git a/cool_seq_tool/schemas.py b/cool_seq_tool/schemas.py
index fae6162c..9a158fe3 100644
--- a/cool_seq_tool/schemas.py
+++ b/cool_seq_tool/schemas.py
@@ -56,7 +56,6 @@ class ResidueMode(str, Enum):
     INTER_RESIDUE     | 0 |   | 1 |   | 2 |   | 3 |
     """
 
-    ZERO = "zero"
     RESIDUE = "residue"
     INTER_RESIDUE = "inter-residue"
 
diff --git a/cool_seq_tool/utils.py b/cool_seq_tool/utils.py
index 130e395c..009052b1 100644
--- a/cool_seq_tool/utils.py
+++ b/cool_seq_tool/utils.py
@@ -21,8 +21,6 @@ def get_inter_residue_pos(
     """
     if residue_mode == ResidueMode.RESIDUE:
         start_pos -= 1
-    elif residue_mode == ResidueMode.ZERO:
-        end_pos += 1
     return start_pos, end_pos
 
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index fa4e3396..5db6250a 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -6,8 +6,6 @@
 def test_get_inter_residue_pos():
     """Test that get_inter_residue_pos function works correctly"""
     expected = (599, 600)
-    resp = get_inter_residue_pos(599, 599, ResidueMode.ZERO)
-    assert resp == expected
 
     resp = get_inter_residue_pos(600, 600, ResidueMode.RESIDUE)
     assert resp == expected
@@ -16,8 +14,6 @@ def test_get_inter_residue_pos():
     assert resp == expected
 
     expected = (746, 751)
-    resp = get_inter_residue_pos(746, 750, ResidueMode.ZERO)
-    assert resp == expected
 
     resp = get_inter_residue_pos(747, 751, ResidueMode.RESIDUE)
     assert resp == expected