Simplify testing

src/genophenocorr/cohort/_cohort_data.py

@@ -72,7 +72,7 @@ def __init__(self, patient_set: typing.Set[Patient], phenotype_set, variant_set,
         self._recessive = recessive
 
     @property
-    def all_patients(self) -> typing.FrozenSet:
+    def all_patients(self) -> typing.FrozenSet[Patient]:
         """
         Returns:
             set: A frozen set of all the Patient objects in the Cohort

src/genophenocorr/phenotype/_phenotype_data.py

@@ -71,7 +71,7 @@ def __hash__(self):
 
     def __str__(self):
         return f"Phenotype(" \
-               "identifier={self.identifier}, " \
+               f"identifier={self.identifier}, " \
                f"name={self.name}, " \
                f"observed={self._observed})"
 

src/genophenocorr/predicate/_all_predicates.py

@@ -17,7 +17,8 @@ class HPOPresentPredicate(PolyPredicate[hpotk.TermId]):
 
                                This is either because the sample is annotated with `q` (exact match),
                                or because one of sample's annotations is a descendant `q` (annotation propagation).
-                               For instance, we tested for a Seizure and the sample did *not* have any Seizure.
+                               For instance, we tested for a Seizure and the sample *had* a Clonic seizure 
+                               (a descendant of Seizure).
                                """)
 
     NOT_OBSERVED = PatientCategory(cat_id=1,

tests/test_fixtures.py

@@ -0,0 +1,114 @@
+import os
+
+import hpotk
+import pytest
+
+from genophenocorr.variant import Variant, VariantCoordinates, TranscriptAnnotation
+from genophenocorr.phenotype import Phenotype
+from genophenocorr.protein import ProteinMetadata, SimpleProteinFeature, FeatureType, FeatureInfo
+from genophenocorr.patient import Patient
+from genophenocorr.cohort import Cohort
+
+
+@pytest.fixture
+def test_cohort() -> Cohort:
+
+    prot = ProteinMetadata(protein_id='NP_037407.4', label='Ankyrin repeat domain-containing protein 11', 
+            protein_features=(SimpleProteinFeature(feature_type=FeatureType.REPEAT, info=FeatureInfo(name='ANK 1', start=167, end=196)), 
+            SimpleProteinFeature(feature_type=FeatureType.REPEAT, info=FeatureInfo(name='ANK 2', start=200, end=229)), 
+            SimpleProteinFeature(feature_type=FeatureType.REPEAT, info=FeatureInfo(name='ANK 3', start=233, end=262)), 
+            SimpleProteinFeature(feature_type=FeatureType.REPEAT, info=FeatureInfo(name='ANK 4', start=266, end=292)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=1, end=90)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=128, end=169)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=289, end=380)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=398, end=647)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=723, end=783)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=881, end=1043)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=1059, end=1393)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=1424, end=1710)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=1814, end=1836)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=1988, end=2019)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Disordered', start=2131, end=2406)), 
+            SimpleProteinFeature(feature_type=FeatureType.REGION, info=FeatureInfo(name='Important for protein degradation', start=2369, end=2663))))
+
+    HetSingleVar = [Variant('16_89279851_-/C', 'insertion', 
+                VariantCoordinates(chrom="16", start=89279849, end=89279851, ref='G', alt='GC', change_length=1, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.6691dup', ['frameshift_variant'], 
+                [9], [prot], 2231, 2231)],genotype='heterozygous')]
+    HetDoubleVar1 = [Variant('16_89284601_GG/A', 'indel', 
+                VariantCoordinates(chrom="16", start=89284600, end=89284602, ref='GG', alt='A', change_length=-1, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.1940_1941delinsT', ['frameshift_variant'], 
+                [9], [prot], 647, 647)],genotype='heterozygous'),
+                Variant('16_89280752_G/T', 'SNV', 
+                VariantCoordinates(chrom="16", start=89280751, end=89280752, ref='G', alt='T', change_length=0, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.5790C>A', ['stop_gained'], 
+                [9], [prot], 1930, 1930)],genotype='heterozygous')]
+    HetDoubleVar2 = [Variant('16_89275128_G/A', 'SNV', 
+                VariantCoordinates(chrom="16", start=89275127, end=89275128, ref='G', alt='A', change_length=0, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.7534C>T', ['missense_variant'], 
+                [10], [prot], 2512, 2512)],genotype='heterozygous'),
+                Variant('16_89279708_AGTGTTCGGGGCGGGGCC/A', 'indel', 
+                VariantCoordinates(chrom="16", start=89279707, end=89279725, ref='AGTGTTCGGGGCGGGGCC', alt='A', change_length=-17, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.6817_6833del', ['frameshift_variant'], 
+                [9], [prot], 2273, 2278)],genotype='heterozygous')]
+    HomoVar = [Variant('16_89279458_TG/T', 'indel', 
+                VariantCoordinates(chrom="16", start=89279457, end=89279459, ref='TG', alt='T', change_length=-1, genotype='homozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.7083del', ['frameshift_variant'], 
+                [9], [prot], 2361, 2362)],genotype='homozygous')]
+    LargeCNV = [Variant('16_89190071_deletion', 'deletion', 
+                VariantCoordinates(chrom="16", start=89190070, end=89439815, ref='N', alt='<DEL>', change_length=4, genotype='heterozygous'),
+                [TranscriptAnnotation('ANKRD11', 'NM_013275.6', None, ['stop_lost', 'feature_truncation', 'coding_sequence_variant', '5_prime_UTR_variant', '3_prime_UTR_variant', 'intron_variant'], 
+                [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], [prot], None, None)],genotype='heterozygous')]
+
+    phenos = get_test_phenotypes()
+
+    patients = (
+        Patient('HetSingleVar',
+                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_F'], phenos['focal_clonic_seizure_T']),
+                variants=HetSingleVar,
+                proteins=[prot]
+                ),
+        Patient('HetDoubleVar1',
+                phenotypes=(phenos['arachnodactyly_T'], phenos['seizure_T'], phenos['spasticity_T']),
+                variants=HetDoubleVar1,
+                proteins=[prot]
+                ),
+        Patient('HetDoubleVar2',
+                phenotypes=(phenos['arachnodactyly_F'], phenos['spasticity_T'], phenos['seizure_T']),
+                variants=HetDoubleVar2,
+                proteins=[prot]
+                ),
+        Patient('HomoVar',
+                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_T'], phenos['seizure_T']),
+                variants=HomoVar,
+                proteins=[prot]
+                ),
+        Patient('LargeCNV',
+                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_T'], phenos['seizure_F']),
+                variants=LargeCNV,
+                proteins=[prot]
+                ),
+    )
+
+    return Cohort.from_patients(patients)
+
+
+def get_test_phenotypes():
+    phenotypes = {}
+
+    phenotypes['arachnodactyly_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", True)
+    phenotypes['seizure_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", True)
+    phenotypes['focal_clonic_seizure_T'] = Phenotype(hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", True)
+    phenotypes['spasticity_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", True)
+    phenotypes['arachnodactyly_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", False)
+    phenotypes['seizure_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", False)
+    phenotypes['spasticity_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", False)
+    phenotypes['focal_clonic_seizure_F'] = Phenotype(hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", False)
+
+    return phenotypes
+
+
+@pytest.fixture
+def toy_hpo() -> hpotk.Ontology:
+    path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'testingDefaults', 'hp.toy.json')
+    return hpotk.ontology.load.obographs.load_ontology(path)