def testBasicAnnotation(self):
''' Test an extremely simple case.
'''
datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09")
m = MutationData()
m.createAnnotation("gene", "TP53")
m.createAnnotation("protein_change", "p.S376C")
m2 = datasource.annotate_mutation(m)
annotationName= "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(m[annotationName].split("|")) == sorted("S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testRangeAnnotation(self):
''' Test a simple case with range.
'''
datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09")
m = MutationData()
m.createAnnotation("gene", "TP53")
m.createAnnotation("protein_change", "p.SLEELEE370_376del") # This is not valid, but does the test.
m2 = datasource.annotate_mutation(m)
annotationName= "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(m[annotationName].split("|")) == sorted("K -> Q (in a sporadic cancer; somatic mutation).|S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testRangeAnnotation(self):
''' Test a simple case with range.
'''
datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09")
m = MutationDataFactory.default_create()
m.createAnnotation("gene", "TP53")
m.createAnnotation("protein_change", "p.SLEELEE370_376del") # This is not valid, but does the test.
m2 = datasource.annotate_mutation(m)
annotationName= "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(m[annotationName].split("|")) == sorted("K -> Q (in a sporadic cancer; somatic mutation).|S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testBasicAnnotation(self):
''' Test an extremely simple case.
'''
datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09")
m = MutationData()
m.createAnnotation("gene", "TP53")
m.createAnnotation("protein_change", "p.S376C")
m.createAnnotation("other_transcripts", "TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Missense_Mutation_p.S244C|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Missense_Mutation_p.S376C")
m2 = datasource.annotate_mutation(m)
annotationName= "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(m[annotationName].split("|")) == sorted("S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
