Set .span property for Interval

python/CHANGELOG.rst

@@ -4,6 +4,9 @@
 
 **Features**
 
+- Genomic intervals returned by python functions are now namedtuples, allowing ``.left``
+  ``.right`` and ``.span`` usage (:user:`hyanwong`, :issue:`784`, :pr:`786`, :pr:`811`)
+
 - :issue:`832` - Add ``metadata_bytes`` method to allow access to raw
   TableCollection metadata (:user:`benjeffery`, :pr:`842`)
 

python/tests/test_highlevel.py

@@ -2363,12 +2363,19 @@ def test_seek(self):
             self.assertRaises(ValueError, tree.seek, bad_position)
 
     def test_interval(self):
-        ts = msprime.simulate(10)
-        tree = ts.first()
-        self.assertEqual(tree.interval[0], 0)
-        self.assertEqual(tree.interval.left, 0)
-        self.assertEqual(tree.interval[1], 1)
-        self.assertEqual(tree.interval.right, 1)
+        ts = msprime.simulate(10, recombination_rate=1, random_seed=1)
+        self.assertGreater(ts.num_trees, 1)
+        breakpoints = list(ts.breakpoints())
+        self.assertEqual(breakpoints[0], 0)
+        self.assertEqual(breakpoints[-1], ts.sequence_length)
+        for i, tree in enumerate(ts.trees()):
+            self.assertAlmostEqual(tree.interval[0], breakpoints[i])
+            self.assertAlmostEqual(tree.interval.left, breakpoints[i])
+            self.assertAlmostEqual(tree.interval[1], breakpoints[i + 1])
+            self.assertAlmostEqual(tree.interval.right, breakpoints[i + 1])
+            self.assertAlmostEqual(
+                tree.interval.span, breakpoints[i + 1] - breakpoints[i]
+            )
 
     def verify_empty_tree(self, tree):
         ts = tree.tree_sequence

python/tskit/trees.py

@@ -58,7 +58,13 @@
     "CoalescenceRecord", ["left", "right", "node", "children", "time", "population"]
 )
 
-Interval = collections.namedtuple("Interval", ["left", "right"])
+BaseInterval = collections.namedtuple("BaseInterval", ["left", "right"])
+
+
+class Interval(BaseInterval):
+    @property
+    def span(self):
+        return self.right - self.left
 
 
 # TODO this interface is rubbish. Should have much better printing options.