fix!: Add support for checking before/after transcript boundaries

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -1169,14 +1169,28 @@ def _get_adjacent_exon(
         :param end: Genomic coordinate of breakpoint
         :return: Exon number corresponding to adjacent exon. Will be 0-based
         """
-        for i in range(len(tx_exons_genomic_coords) - 1):
+        # 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
+
+        if strand == Strand.POSITIVE:
+            if bp < tx_exons_genomic_coords[0].alt_start_i:
+                return 0
+            if bp > tx_exons_genomic_coords[exon_list_len].alt_end_i:
+                return exon_list_len
+        if strand == Strand.NEGATIVE:
+            if bp > tx_exons_genomic_coords[0].alt_end_i:
+                return 0
+            if bp < tx_exons_genomic_coords[exon_list_len].alt_start_i:
+                return exon_list_len
+
+        for i in range(exon_list_len):
             exon = tx_exons_genomic_coords[i]
             if start == exon.alt_start_i:
                 break
             if end == exon.alt_end_i:
                 break
             next_exon = tx_exons_genomic_coords[i + 1]
-            bp = start if start else end
             if strand == Strand.POSITIVE:
                 lte_exon = exon
                 gte_exon = next_exon

tests/mappers/test_exon_genomic_coords.py

@@ -840,6 +840,32 @@ async def test_get_adjacent_exon(
     )
     assert resp == 4
 
+    # Check cases where breakpoint occurs in before/after transcript boundaries
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80486220,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80526285,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 5
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154192110,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154161809,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 9
+
 
 def test_is_exonic_breakpoint(test_egc_mapper, nm_001105539_exons_genomic_coords):
     """Test is breakpoint occurs on exon"""