From afeb69dff3555c65b1f9d6add57b153ea78030ee Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Fri, 21 Jun 2024 13:03:20 +0100
Subject: [PATCH] add locations_overlap to utils

---
 src/pydna/utils.py         | 25 +++++++++++++++++++++++++
 tests/test_module_utils.py | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)

diff --git a/src/pydna/utils.py b/src/pydna/utils.py
index 08078f87..a007e5a8 100644
--- a/src/pydna/utils.py
+++ b/src/pydna/utils.py
@@ -704,6 +704,31 @@ def location_boundaries(loc: _Union[_sl, _cl]):
         return loc.parts[0].start, loc.parts[-1].end
 
 
+def locations_overlap(loc1: _Union[_sl, _cl], loc2: _Union[_sl, _cl], seq_len):
+    start1, end1 = location_boundaries(loc1)
+    start2, end2 = location_boundaries(loc2)
+
+    boundaries1 = [(start1, end1)]
+    boundaries2 = [(start2, end2)]
+
+    if start1 > end1:
+        boundaries1 = [
+            [start1, end1 + seq_len],
+            [start1 - seq_len, end1],
+        ]
+    if start2 > end2:
+        boundaries2 = [
+            [start2, end2 + seq_len],
+            [start2 - seq_len, end2],
+        ]
+
+    for b1, b2 in _itertools.product(boundaries1, boundaries2):
+        if b1[0] < b2[1] and b1[1] > b2[0]:
+            return True
+
+    return False
+
+
 if __name__ == "__main__":
     cached = _os.getenv("pydna_cached_funcs", "")
     _os.environ["pydna_cached_funcs"] = ""
diff --git a/tests/test_module_utils.py b/tests/test_module_utils.py
index 47f1c8e4..d733720d 100644
--- a/tests/test_module_utils.py
+++ b/tests/test_module_utils.py
@@ -475,5 +475,41 @@ def test_shift_location():
         assert shift_location(shift_location(loc, 1, 6), -1, 6) == loc
 
 
+def test_locations_overlap():
+    from pydna.utils import locations_overlap, shift_location
+    from Bio.SeqFeature import SimpleLocation
+
+    # exact        =====          |
+    # greater    =========        |
+    # inner         ==            |
+    # right         =====         |
+    # left        =====           |
+    # main         =====          |
+    #         -----------------------------------------
+    #         0123456789
+    main_overlap = SimpleLocation(5, 10)
+    inner_overlap = SimpleLocation(6, 8)
+    right_overlap = SimpleLocation(6, 11)
+    left_overlap = SimpleLocation(4, 9)
+    exact_overlap = SimpleLocation(5, 10)
+    greater_overlap = SimpleLocation(3, 12)
+    no_overlap_left = SimpleLocation(0, 5)
+    no_overlap_right = SimpleLocation(11, 15)
+
+    overlapping_locations = [inner_overlap, right_overlap, left_overlap, exact_overlap, greater_overlap]
+    non_overlapping_locations = [no_overlap_left, no_overlap_right]
+
+    for shift in range(20):
+        main_shifted = shift_location(main_overlap, shift, 20)
+        for loc in overlapping_locations:
+            loc_shifted = shift_location(loc, shift, 20)
+            assert locations_overlap(main_shifted, loc_shifted, 20)
+        for loc in non_overlapping_locations:
+            loc_shifted = shift_location(loc, shift, 20)
+            assert not locations_overlap(main_shifted, loc_shifted, 20)
+
+
+
+
 if __name__ == "__main__":
     pytest.main([__file__, "-vv", "-s"])