Improve generating the polypredicate question.

docs/tutorial.rst

@@ -171,7 +171,7 @@ in the individuals of the *TBX5* cohort.
 ...     ),
 ...     group_names=('Missense', 'Frameshift'),
 ... )
->>> gt_predicate.get_question()
+>>> gt_predicate.display_question()
 'Genotype group: Missense, Frameshift'
 
 .. note::

docs/user-guide/predicates.rst

@@ -300,7 +300,7 @@ for assigning a patient into a genotype group:
 
 >>> from gpsea.analysis.predicate.genotype import ModeOfInheritancePredicate
 >>> gt_predicate = ModeOfInheritancePredicate.autosomal_recessive(is_frameshift_or_stop_gain)
->>> gt_predicate.get_question()
+>>> gt_predicate.display_question()
 'Which genotype group does the patient fit in: HOM_REF, HET, BIALLELIC_ALT'
 
 The `gt_predicate` can be used in downstream analysis, such as in :class:
@@ -337,7 +337,7 @@ for testing if the individual has at least one missense vs. frameshift vs. synon
 ...     ),
 ...     group_names=('Missense', 'Frameshift', 'Synonymous'),
 ... )
->>> gt_predicate.get_question()
+>>> gt_predicate.display_question()
 'Genotype group: Missense, Frameshift, Synonymous'
 
 
@@ -380,8 +380,8 @@ to test for a presence of `Abnormal lens morphology <https://hpo.jax.org/browse/
 ...     hpo=hpo,
 ...     query=query,
 ... )
->>> pheno_predicate.get_question()
-'Is Abnormal lens morphology present in the patient?'
+>>> pheno_predicate.display_question()
+'Is Abnormal lens morphology present in the patient: Yes, No'
 
 
 TODO: explain ``missing_implies_phenotype_excluded``

docs/user-guide/stats.rst

@@ -138,7 +138,7 @@ we expect the autosomal dominant mode of inheritance:
 
 >>> from gpsea.analysis.predicate.genotype import ModeOfInheritancePredicate
 >>> gt_predicate = ModeOfInheritancePredicate.autosomal_dominant(is_frameshift)
->>> gt_predicate.get_question()
+>>> gt_predicate.display_question()
 'Which genotype group does the patient fit in: HOM_REF, HET'
 
 `gt_predicate` will assign the patients with no frameshift variant allele into `HOM_REF` group
@@ -409,7 +409,7 @@ The genotype predicate will bin the patient into two groups: a point mutation gr
 ...     predicates=(point_mutation, lof_mutation),
 ...     group_names=('Point', 'LoF'),
 ... )
->>> gt_predicate.get_question()
+>>> gt_predicate.display_question()
 'Genotype group: Point, LoF'
 
 

src/gpsea/analysis/_api.py

@@ -189,7 +189,7 @@ def summarize(
         # Column index: multiindex of counts and percentages for all genotype predicate groups
         geno_idx = pd.MultiIndex.from_product(
             iterables=(self._geno_predicate.get_categories(), ('Count', 'Percent')),
-            names=(self._geno_predicate.get_question(), None),
+            names=(self._geno_predicate.get_question_base(), None),
         )
 
         # We'll fill this frame with data

src/gpsea/analysis/_gp_analysis.py

@@ -63,11 +63,11 @@ def apply_predicates_on_patients(
                 data=0,
                 index=pd.Index(
                     data=ph_predicate.get_categories(),
-                    name=ph_predicate.get_question(),
+                    name=ph_predicate.get_question_base(),
                 ),
                 columns=pd.Index(
                     data=gt_predicate.get_categories(),
-                    name=gt_predicate.get_question(),
+                    name=gt_predicate.get_question_base(),
                 ),
             )
 

src/gpsea/analysis/pcats/_impl.py

@@ -64,11 +64,11 @@ def apply_predicates_on_patients(
                 data=0,
                 index=pd.Index(
                     data=ph_predicate.get_categories(),
-                    name=ph_predicate.get_question(),
+                    name=ph_predicate.get_question_base(),
                 ),
                 columns=pd.Index(
                     data=gt_predicate.get_categories(),
-                    name=gt_predicate.get_question(),
+                    name=gt_predicate.get_question_base(),
                 ),
             )
 
@@ -198,7 +198,7 @@ def summarize(
         gt_idx = pd.MultiIndex.from_product(
             # TODO: fix the below
             iterables=(self._gt_predicate.get_categories(), ("Count", "Percent")),
-            names=(self._gt_predicate.get_question(), None),
+            names=(self._gt_predicate.get_question_base(), None),
         )
 
         # We'll fill this frame with data

src/gpsea/analysis/predicate/_api.py

@@ -154,6 +154,12 @@ def get_categories(self) -> typing.Iterator[PatientCategory]:
         """
         return (c.category for c in self.get_categorizations())
 
+    def get_category_names(self) -> typing.Iterator[str]:
+        """
+        Get an iterator with names of the :class:`PatientCategory` items that the predicate can produce.
+        """
+        return (cat.name for cat in self.get_categories())
+
     def get_category(
         self,
         cat_id: int,
@@ -182,12 +188,21 @@ def get_category_name(
         return self.get_category(cat_id).name
 
     @abc.abstractmethod
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         """
         Prepare a `str` with the question the predicate can answer.
         """
         pass
 
+    def display_question(self) -> str:
+        """
+        Prepare the question which the predicate can answer.
+
+        The question includes the question base and the category names
+        """
+        cat_names = ', '.join(self.get_category_names())
+        return f'{self.get_question_base()}: {cat_names}'
+
     @abc.abstractmethod
     def test(self, patient: Patient) -> typing.Optional[C]:
         """

src/gpsea/analysis/predicate/genotype/_api.py

@@ -77,8 +77,8 @@ def __init__(
     def get_categorizations(self) -> typing.Sequence[Categorization]:
         return self._allowed
 
-    def get_question(self) -> str:
-        return self._predicate.get_question()
+    def get_question_base(self) -> str:
+        return self._predicate.get_question_base()
 
     def test(self, patient: Patient) -> typing.Optional[Categorization]:
         cat = self._predicate.test(patient)

src/gpsea/analysis/predicate/genotype/_gt_predicates.py

@@ -39,7 +39,7 @@ def get_categorizations(self) -> typing.Sequence[Categorization]:
             AlleleCountingGenotypeBooleanPredicate.NO,
         )
 
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         return self._allele_counter.get_question()
 
     def test(self, patient: Patient) -> typing.Optional[Categorization]:
@@ -92,13 +92,12 @@ def __init__(
     ):
         self._counters = tuple(counters)
         self._categorizations = tuple(categorizations)
-        group_names = ", ".join(c.category.name for c in self._categorizations)
-        self._question = f"Genotype group: {group_names}"
+        self._question = "Genotype group"
 
     def get_categorizations(self) -> typing.Sequence[Categorization]:
         return self._categorizations
 
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         return self._question
 
     def test(self, patient: Patient) -> typing.Optional[Categorization]:
@@ -132,7 +131,7 @@ def __hash__(self) -> int:
         )
 
     def __str__(self) -> str:
-        return self.get_question()
+        return self.get_question_base()
 
     def __repr__(self) -> str:
         return (
@@ -194,7 +193,7 @@ def __init__(
     ):
         self._allele_counter = allele_counter
 
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         return self._allele_counter.get_question()
 
     def test(self, patient: Patient) -> typing.Optional[Categorization]:
@@ -558,14 +557,12 @@ def __init__(
         issues = ModeOfInheritancePredicate._check_categorizations(self._categorizations)
         if issues:
             raise ValueError('Cannot create predicate: {}'.format(', '.join(issues)))
-        self._question = 'Which genotype group does the patient fit in: {}'.format(
-            ', '.join(cat.category.name for cat in self._categorizations),
-        )
+        self._question = 'Which genotype group does the patient fit in'
 
     def get_categorizations(self) -> typing.Sequence[Categorization]:
         return self._categorizations
 
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         return self._question
 
     def test(

src/gpsea/analysis/predicate/phenotype/_pheno.py

@@ -131,8 +131,8 @@ def __init__(
         # Some tests depend on the order of `self._categorizations`.
         self._categorizations = (self._phenotype_observed, self._phenotype_excluded)
 
-    def get_question(self) -> str:
-        return f"Is {self._query_label} present in the patient?"
+    def get_question_base(self) -> str:
+        return f"Is {self._query_label} present in the patient"
 
     @property
     def phenotype(self) -> hpotk.TermId:
@@ -222,7 +222,7 @@ def __init__(self, disease_id_query: hpotk.TermId):
             phenotype=disease_id_query,
         )
 
-    def get_question(self) -> str:
+    def get_question_base(self) -> str:
         return f"Was {self._query} diagnosed in the patient"
 
     @property

tests/analysis/predicate/genotype/test_gt_predicates.py

@@ -36,8 +36,8 @@ def test_get_question(
         self,
         predicate: GenotypePolyPredicate,
     ):
-        question = predicate.get_question()
-        assert question == "Genotype group: Point, LoF"
+        question = predicate.get_question_base()
+        assert question == "Genotype group"
 
     def test_get_categorizations(
         self,