From 78ab1136805b9d99c000ceeccca21aff523301fc Mon Sep 17 00:00:00 2001
From: Jeremy Arbesfeld <50678786+jarbesfeld@users.noreply.github.com>
Date: Thu, 12 Dec 2024 12:19:11 -0500
Subject: [PATCH] fix: Check to see if there is only one exon in a transcript
 when selecting the adjacent exon (#386)

---
 src/cool_seq_tool/mappers/exon_genomic_coords.py |  5 +++++
 tests/conftest.py                                | 15 +++++++++++++++
 tests/mappers/test_exon_genomic_coords.py        | 14 +++++++++++++-
 3 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
index 82d4a72..056d1d7 100644
--- a/src/cool_seq_tool/mappers/exon_genomic_coords.py
+++ b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -1169,6 +1169,10 @@ def _get_adjacent_exon(
         :param end: Genomic coordinate of breakpoint
         :return: Exon number corresponding to adjacent exon. Will be 0-based
         """
+        # If a transcript has only one exon, return 0
+        if len(tx_exons_genomic_coords) == 1:
+            return 0
+
         # Check if a breakpoint occurs before/after the transcript boundaries
         bp = start if start else end
         exon_list_len = len(tx_exons_genomic_coords) - 1
@@ -1199,6 +1203,7 @@ def _get_adjacent_exon(
                 gte_exon = exon
             if bp >= lte_exon.alt_end_i and bp <= gte_exon.alt_start_i:
                 break
+
         # Return current exon if end position is provided, next exon if start position
         # is provided.
         return exon.ord if end else exon.ord + 1
diff --git a/tests/conftest.py b/tests/conftest.py
index d37c2ec..d44f391 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -277,6 +277,21 @@ def nm_001105539_exons_genomic_coords():
     ]
 
 
+@pytest.fixture(scope="session")
+def mm_001005183_1_exons():
+    """Create test fixture for NM_001005183.1 exons and genomic coordinates"""
+    return [
+        _ExonCoord(
+            ord=0,
+            tx_start_i=0,
+            tx_end_i=939,
+            alt_start_i=55426253,
+            alt_end_i=55427192,
+            alt_strand=Strand.POSITIVE,
+        )
+    ]
+
+
 @pytest.fixture(scope="session")
 def tpm3_1_8_start_genomic():
     """Create test fixture for genomic data for exon 1, 8"""
diff --git a/tests/mappers/test_exon_genomic_coords.py b/tests/mappers/test_exon_genomic_coords.py
index c779953..5cdfb1f 100644
--- a/tests/mappers/test_exon_genomic_coords.py
+++ b/tests/mappers/test_exon_genomic_coords.py
@@ -806,7 +806,10 @@ async def test_get_start_end_exon_coords(test_egc_mapper):
 
 @pytest.mark.asyncio()
 async def test_get_adjacent_exon(
-    test_egc_mapper, nm_152263_exons_genomic_coords, nm_001105539_exons_genomic_coords
+    test_egc_mapper,
+    nm_152263_exons_genomic_coords,
+    nm_001105539_exons_genomic_coords,
+    mm_001005183_1_exons,
 ):
     """Test that get_adjacent_exon works properly"""
     resp = test_egc_mapper._get_adjacent_exon(
@@ -866,6 +869,15 @@ async def test_get_adjacent_exon(
     )
     assert resp == 9
 
+    # Check cases where transcript only has one exon and breakpoint does not occur
+    # exon
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=mm_001005183_1_exons,
+        start=55411058,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+
 
 def test_is_exonic_breakpoint(test_egc_mapper, nm_001105539_exons_genomic_coords):
     """Test is breakpoint occurs on exon"""