Add site.alleles method

Deliberately returns an (unordered) set

Author: hyanwong

python/CHANGELOG.rst

@@ -7,6 +7,10 @@
 - SVG drawing routines now return a special string object that is automatically
   rendered in a Jupyter notebook (:user:`hyanwong`, :pr:`2377`)
 
+**Features**
+
+- New ``Site.alleles()`` method (:user:`hyanwong`, :issue:`2380`, :pr:`2385`)
+
 
 --------------------
 [0.5.0] - 2022-06-22

python/tests/test_highlevel.py

@@ -2592,6 +2592,29 @@ def test_individual_properties(self, n):
         self.verify_individual_properties(ts)
 
 
+class TestSiteAlleles:
+    def test_no_mutations(self):
+        tables = tskit.TableCollection(sequence_length=1)
+        tables.sites.add_row(0, ancestral_state="")
+        site = tables.tree_sequence().site(0)
+        assert site.alleles == {""}
+
+    @pytest.mark.parametrize("k", range(5))
+    def test_k_mutations(self, k):
+        tables = tskit.TableCollection(sequence_length=1)
+        tables.sites.add_row(0, ancestral_state="ABC")
+        tables.nodes.add_row(1, 0)
+        tables.nodes.add_row(1, 0)  # will not have any mutations => missing
+        for j in range(k):
+            tables.mutations.add_row(site=0, node=0, derived_state=str(j))
+        ts = tables.tree_sequence()
+        variant = next(ts.variants())
+        assert variant.has_missing_data
+        assert len(variant.site.alleles) == k + 1
+        assert "ABC" in variant.site.alleles
+        assert variant.site.alleles == set(variant.alleles[:-1])
+
+
 class TestEdgeDiffs:
     @pytest.mark.parametrize("ts", get_example_tree_sequences())
     def test_correct_trees_forward(self, ts):

python/tskit/trees.py

@@ -357,6 +357,22 @@ def __eq__(self, other):
             and self.metadata == other.metadata
         )
 
+    @property
+    def alleles(self) -> set[str]:
+        """
+        Return the set of all the alleles defined at this site
+
+        .. note::
+            This deliberately returns an (unordered) *set* of the possible allelic
+            states (as defined by the site's ancestral allele and its associated
+            mutations). If you wish to obtain an (ordered) *list* of alleles, for
+            example to translate the numeric genotypes at a site into allelic states,
+            you should instead use ``.alleles`` attribute of the :class:`Variant` class,
+            which unlike this attribute includes ``None`` as a state when there is
+            missing data at a site.
+        """
+        return {self.ancestral_state} | {m.derived_state for m in self.mutations}
+
 
 @metadata_module.lazy_decode()
 @dataclass