Locations overlap

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.flake8",
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,15 @@
+{
+    "files.exclude": {
+        "**/.git": true,
+        "**/.svn": true,
+        "**/.hg": true,
+        "**/CVS": true,
+        "**/.DS_Store": true,
+        "**/*.pyc": true,
+        "**/__pycache__": true
+    },
+    // Set flake8 path
+    "flake8.path": [".venv/bin/flake8"],
+    "black-formatter.path": [".venv/bin/black"],
+    "python.defaultInterpreterPath": ".venv/bin/python",
+}

README.md

@@ -264,7 +264,7 @@ or by `pip install pyparsing requests cai2 scipy matplotlib pillow`
 
 ## Contributing
 
-Please direct pull requests towards the `develop` branch.
+Please direct pull requests towards the `dev_bjorn` branch.
 
 
 ### Local development
@@ -273,6 +273,7 @@ Please direct pull requests towards the `develop` branch.
 
     ```bash
     # If you want the virtual environment to be created in this folder
+    # (this is now the default, see `poetry.toml`)
     poetry config virtualenvs.in-project true
 
     # Install dependencies (extras are required for tests to pass)
@@ -281,16 +282,17 @@ Please direct pull requests towards the `develop` branch.
     # Activate virtual environment
     poetry shell
     ```
-
 2. Make your changes.
 3. Add the necessary tests in `tests/`.
 4. Run the tests from the root directory with `python run_test.py`.
+5. Install `pre-commit` hooks if you haven't by running `pre-commit install`. `pre-commit` should be available in the environment, since it is installed by poetry.
+6. Make a PR.
 
 #### Building the documentation locally
 
 Below the commands to run a local sphinx server that auto-updated when files are changed.
 
-```
+```bash
 # Install docs dependency group
 poetry install --with docs
 

poetry.toml

@@ -0,0 +1,2 @@
+[virtualenvs]
+in-project = true

pyproject.toml

@@ -35,24 +35,24 @@ version = "6.0.0-a.24.post.17+b7b559bd66"
 [tool.poetry.dependencies]
 appdirs = ">=1.4.4"
 biopython = ">=1.80"
-cai2 = {version = ">=1.0.5", optional = true}
-matplotlib = {version = ">=3.4.3", optional = true}
+cai2 = { version = ">=1.0.5", optional = true }
+matplotlib = { version = ">=3.4.3", optional = true }
 networkx = ">=2.8.8"
 numpy = [
-  {version = ">1.26", python = ">=3.9"},
-  {version = "<1.24", python = "<3.9"},
+  { version = ">1.26", python = ">=3.9" },
+  { version = "<1.24", python = "<3.9" },
 ]
-pillow = {version = ">=8.4.0", optional = true}
+pillow = { version = ">=8.4.0", optional = true }
 prettytable = ">=3.5.0"
 pydivsufsort = ">=0.0.14"
 pyfiglet = "0.8.post1"
-pyparsing = {version = ">=2.4.7", optional = true}
-pyperclip = {version = ">=1.8.2", optional = true}
+pyparsing = { version = ">=2.4.7", optional = true }
+pyperclip = { version = ">=1.8.2", optional = true }
 python = ">=3.8,<4.0"
-requests = {version = ">=2.26.0", optional = true}
+requests = { version = ">=2.26.0", optional = true }
 scipy = [
-  {version = ">=1.11.3", python = ">=3.12", optional = true},
-  {version = ">=1.9.3", python = "<3.12", optional = true},
+  { version = ">=1.11.3", python = ">=3.12", optional = true },
+  { version = ">=1.9.3", python = "<3.12", optional = true },
 ]
 seguid = ">=0.0.5"
 [tool.poetry.extras]
@@ -62,10 +62,7 @@ express = ["cai2"]
 gel = ["scipy", "matplotlib", "pillow"]
 [build-system]
 build-backend = "poetry_dynamic_versioning.backend"
-requires = [
-  "poetry-core",
-  "poetry-dynamic-versioning",
-]
+requires = ["poetry-core", "poetry-dynamic-versioning"]
 [tool.poetry-dynamic-versioning]
 enable = true
 style = "semver"
@@ -87,13 +84,20 @@ numpydoc = "^1.6.0"
 sphinx-autobuild = "^2021.3.14"
 sphinx-rtd-theme = ">=1.3,<3.0"
 
+
+[tool.poetry.group.dev.dependencies]
+autopep8 = "^2.1.0"
+black = "^24.4.2"
+flake8-bugbear = [{ version = ">=24.4.21", python = ">=3.8.1" }]
+pre-commit = [
+  { version = ">3.6", python = ">=3.9" },
+  { version = "<3.6", python = "<3.9" },
+]
+
 [tool.pytest.ini_options]
 minversion = "6.0.2"
 python_files = "test_*.py"
-testpaths = [
-  "tests",
-  "src",
-]
+testpaths = ["tests", "src"]
 [tool.black]
 include = '\.pyi?$'
 line-length = 119

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"] = ""

tests/test_module_dseq.py

@@ -827,6 +827,7 @@ def test_left_end_position():
 
 def test_apply_cut():
     from pydna.dseq import Dseq
+    from Bio.Restriction import EcoRI, BamHI
 
     seq = Dseq('aaGAATTCaa', circular=False)
 
@@ -876,31 +877,31 @@ def test_apply_cut():
     # Overlapping cuts should return an error
     seq = Dseq('aaGAATTCaa', circular=True)
     first_cuts = [
-        ((3, -4), None),
-        ((7, 4), None),
+        ((3, -4), BamHI),
+        ((7, 4), BamHI),
         # Spanning the origin
-        ((9, -8), None),
-        ((8, 8), None),
+        ((9, -8), BamHI),
+        ((8, 8), BamHI),
     ]
 
     overlapping_cuts = [
-        ((4, -4), None),
-        ((2, -4), None),
-        ((2, -6), None),
-        ((8, 4), None),
-        ((6, 4), None),
-        ((8, 6), None),
+        ((4, -4), EcoRI),
+        ((2, -4), EcoRI),
+        ((2, -6), EcoRI),
+        ((8, 4), EcoRI),
+        ((6, 4), EcoRI),
+        ((8, 6), EcoRI),
         # Spanning the origin
-        ((7, -8), None),
-        ((6, 8), None),
+        ((7, -8), EcoRI),
+        ((6, 8), EcoRI),
     ]
 
     for first_cut in first_cuts:
         for second_cut in overlapping_cuts:
             try:
                 seq.apply_cut(first_cut, second_cut)
             except ValueError as e:
-                assert e.args[0] == 'Cuts overlap'
+                assert e.args[0] == 'Cuts by BamHI EcoRI overlap.'
             else:
                 print(first_cut, second_cut)
                 assert False, 'Expected ValueError'

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"])