Fix #72 : Merge remote-tracking branch 'godotgildor/feature/add_locat…

…ion_comparisons' into dev

.travis.yml

@@ -3,10 +3,8 @@ python:
   - "3.9"
 # command to install dependencies
 install:
-  - pip install coveralls pytest-cov pytest
-  - pip install matplotlib primer3-py genome_collector geneblocks
   - sudo apt-get install ncbi-blast+ bowtie
-  - pip install -e .[reports]
+  - pip install -e .[reports,tests]
 # command to run tests
 script:
   - python -m pytest -v --cov dnachisel --cov-report term-missing

dnachisel/Location.py

@@ -3,11 +3,13 @@
 The class has useful methods for finding overlaps between locations, extract
 a subsequence from a sequence, etc.
 """
+from functools import total_ordering
 
 from .biotools import reverse_complement
 from Bio.SeqFeature import SeqFeature, FeatureLocation
 
 
+@total_ordering
 class Location:
     """Represent a segment of a sequence, with a start, end, and strand.
 
@@ -93,10 +95,10 @@ def indices(self):
         result = list(range(self.start, self.end))
         return result if (self.strand != -1) else result[::-1]
 
-    def __geq__(self, other):
-        """Greater than."""
-        return self.to_tuple() >= other.to_tuple()
-
+    def __eq__(self, other):
+        """Equal to."""
+        return self.to_tuple() == other.to_tuple()
+    
     def __lt__(self, other):
         """Lower than."""
         return self.to_tuple() < other.to_tuple()

setup.py

@@ -46,6 +46,15 @@
             "matplotlib",
             "dna_features_viewer",
             "pandas",
+        ],
+        "tests": [
+            "coveralls",
+            "geneblocks",
+            "genome_collector",
+            "matplotlib",
+            "primer3-py",
+            "pytest",
+            "pytest-cov",
         ]
     },
 )

tests/test_Location.py

@@ -0,0 +1,51 @@
+from dnachisel.Location import Location
+
+import pytest
+
+@pytest.mark.parametrize("location_1,location_2,expected_result", [
+        (Location(0, 1), Location(0, 1), True),
+        (Location(0, 1), Location(1, 1), False),
+        (Location(0, 1), Location(0, 1, 1), False),
+        (Location(0, 1, 1), Location(0, 1, 1), True),
+        (Location(0, 1, 0), Location(0, 1, 0), True),
+        (Location(0, 1), Location(1, 0), False),
+        (Location(0, 1), Location(1, 0, 1), False),
+        (Location(0, 1), Location(1, 0, 0), False),
+    ]
+)
+def test___eq__(location_1: Location, location_2: Location, expected_result: bool):
+    assert (location_1 == location_2) == expected_result
+
+@pytest.mark.parametrize("location_1,location_2,expected_result", [
+        (Location(0, 1), Location(0, 1), True),
+        (Location(0, 1), Location(1, 1), False),
+        (Location(1, 0), Location(0, 1), True),
+        (Location(1, 0, 1), Location(1, 0), True),
+        (Location(0, 1), Location(0, 1, 1), False),
+        (Location(0, 1, 1), Location(0, 1), True),
+        (Location(0, 1, 1), Location(0, 1, 1), True),
+        (Location(0, 1, 0), Location(0, 1, 0), True),
+        (Location(0, 1), Location(1, 0), False),
+        (Location(0, 1), Location(1, 0, 1), False),
+        (Location(0, 1), Location(1, 0, 0), False),
+    ]
+)
+def test___ge__(location_1: Location, location_2: Location, expected_result: bool):
+    assert (location_1 >= location_2) == expected_result
+
+@pytest.mark.parametrize("location_1,location_2,expected_result", [
+        (Location(0, 1), Location(0, 1), False),
+        (Location(0, 1), Location(1, 1), True),
+        (Location(1, 0), Location(0, 1), False),
+        (Location(1, 0, 1), Location(1, 0), False),
+        (Location(0, 1), Location(0, 1, 1), True),
+        (Location(0, 1, 1), Location(0, 1), False),
+        (Location(0, 1, 1), Location(0, 1, 1), False),
+        (Location(0, 1, 0), Location(0, 1, 0), False),
+        (Location(0, 1), Location(1, 0), True),
+        (Location(0, 1), Location(1, 0, 1), True),
+        (Location(0, 1), Location(1, 0, 0), True),
+    ]
+)
+def test___lt__(location_1: Location, location_2: Location, expected_result: bool):
+    assert (location_1 < location_2) == expected_result