From 93bc9107f9f95f3108671367b69774eb28ab05f4 Mon Sep 17 00:00:00 2001 From: Yasemin Bridges Date: Wed, 4 Oct 2023 11:10:08 +0100 Subject: [PATCH] adding tests for creating the input file --- tests/test_create_input_data.py | 166 ++++++++++++++++++++++++++++++++ 1 file changed, 166 insertions(+) create mode 100644 tests/test_create_input_data.py diff --git a/tests/test_create_input_data.py b/tests/test_create_input_data.py new file mode 100644 index 0000000..8a05701 --- /dev/null +++ b/tests/test_create_input_data.py @@ -0,0 +1,166 @@ +import unittest +from pathlib import Path + +from phenopackets import ( + Diagnosis, + Disease, + Family, + File, + GeneDescriptor, + GenomicInterpretation, + Individual, + Interpretation, + MetaData, + OntologyClass, + Pedigree, + Phenopacket, + PhenotypicFeature, + Resource, + VariantInterpretation, + VariationDescriptor, + VcfRecord, +) +from pheval.utils.phenopacket_utils import PhenopacketUtil + +from pheval_gado.prepare.create_input_data import ( + get_list_of_phenotypic_features, create_case_id_from_phenopacket, + create_entry_for_phenopacket +) + +interpretations = [ + Interpretation( + id="test-subject-1-int", + progress_status="SOLVED", + diagnosis=Diagnosis( + disease=OntologyClass(id="OMIM:219700", label="Cystic Fibrosis"), + genomic_interpretations=[ + GenomicInterpretation( + subject_or_biosample_id="test-subject-1", + interpretation_status=4, + variant_interpretation=VariantInterpretation( + acmg_pathogenicity_classification="NOT_PROVIDED", + therapeutic_actionability="UNKNOWN_ACTIONABILITY", + variation_descriptor=VariationDescriptor( + gene_context=GeneDescriptor( + value_id="ENSG00000102302", + symbol="FGD1", + alternate_ids=[ + "HGNC:3663", + "ncbigene:2245", + "ensembl:ENSG00000102302", + "symbol:FGD1", + ], + ), + vcf_record=VcfRecord( + genome_assembly="GRCh37", + chrom="X", + pos=54492285, + ref="C", + alt="T", + ), + allelic_state=OntologyClass( + id="GENO:0000134", + label="hemizygous", + ), + ), + ), + ), + GenomicInterpretation( + subject_or_biosample_id="test-subject-1", + interpretation_status=4, + variant_interpretation=VariantInterpretation( + acmg_pathogenicity_classification="NOT_PROVIDED", + therapeutic_actionability="UNKNOWN_ACTIONABILITY", + variation_descriptor=VariationDescriptor( + gene_context=GeneDescriptor( + value_id="ENSG00000176225", + symbol="RTTN", + alternate_ids=[ + "HGNC:18654", + "ncbigene:25914", + "ensembl:ENSG00000176225", + "symbol:RTTN", + ], + ), + vcf_record=VcfRecord( + genome_assembly="GRCh37", + chrom="18", + pos=67691994, + ref="G", + alt="A", + ), + allelic_state=OntologyClass( + id="GENO:0000402", label="compound heterozygous" + ), + ), + ), + ), + ], + ), + ) +] +phenotypic_features_with_excluded = [ + PhenotypicFeature(type=OntologyClass(id="HP:0000256", label="Macrocephaly")), + PhenotypicFeature(type=OntologyClass(id="HP:0002059", label="Cerebral atrophy")), + PhenotypicFeature(type=OntologyClass(id="HP:0100309", label="Subdural hemorrhage")), + PhenotypicFeature(type=OntologyClass(id="HP:0003150", label="Glutaric aciduria")), + PhenotypicFeature(type=OntologyClass(id="HP:0001332", label="Dystonia")), + PhenotypicFeature( + type=OntologyClass(id="HP:0008494", label="Inferior lens subluxation"), excluded=True + ), +] + +diseases = [Disease(term=OntologyClass(id="OMIM:219700", label="Cystic Fibrosis"))] + +phenopacket_files = [ + File( + uri="test/path/to/test_1.vcf", + file_attributes={"fileFormat": "vcf", "genomeAssembly": "GRCh37"}, + ), + File( + uri="test_1.ped", + file_attributes={"fileFormat": "PED", "genomeAssembly": "GRCh37"}, + ), +] +phenopacket_metadata = MetaData( + created_by="pheval-converter", + resources=[ + Resource( + id="hp", + name="human phenotype ontology", + url="http://purl.obolibrary.org/obo/hp.owl", + version="hp/releases/2019-11-08", + namespace_prefix="HP", + iri_prefix="http://purl.obolibrary.org/obo/HP_", + ) + ], + phenopacket_schema_version="2.0", +) + +phenopacket = Phenopacket( + id="test-subject", + subject=Individual(id="test-subject-1", sex=1), + phenotypic_features=phenotypic_features_with_excluded, + interpretations=interpretations, + diseases=diseases, + files=phenopacket_files, + meta_data=phenopacket_metadata, +) + + +class TestGetListOfPhenotypicFeatures(unittest.TestCase): + def test_get_list_of_phenotypic_features(self): + self.assertEqual(get_list_of_phenotypic_features(PhenopacketUtil(phenopacket)), + ['HP:0000256', 'HP:0002059', 'HP:0100309', 'HP:0003150', 'HP:0001332']) + + +class TestCreateCaseIDFromPhenopacket(unittest.TestCase): + def test_create_case_id_from_phenopacket(self): + self.assertEqual(create_case_id_from_phenopacket(Path("/path/to/Phenopacket-case-1.json")), + "Phenopacket-case-1") + + +class TestCreateEntryForPhenopacket(unittest.TestCase): + def test_create_entry_for_phenopacket(self): + self.assertEqual(create_entry_for_phenopacket(Path("/path/to/Phenopacket-case-1.json"), phenopacket), + ['Phenopacket-case-1', 'HP:0000256', 'HP:0002059', 'HP:0100309', 'HP:0003150', 'HP:0001332'])