def test_gene_fusion_missing_implicit(self): """Test serialization of a gene fusion to BEL with a implicit missing fusion ranges.""" dsl = GeneFusion( Gene('HGNC', 'TMPRSS2'), Gene('HGNC', 'ERG'), ) self.assertEqual('g(fus(HGNC:TMPRSS2, "?", HGNC:ERG, "?"))', dsl.as_bel())
def test_fusion_specified(self, mock): node_data = GeneFusion( Gene('HGNC', 'TMPRSS2'), Gene('HGNC', 'ERG'), EnumeratedFusionRange('c', 1, 79), EnumeratedFusionRange('c', 312, 5034), ) self._help_reconstitute(node_data, 1, 0)
def test_GeneFusion(self): """Test serialization of a gene fusion to BEL with a explicit fusion ranges.""" dsl = GeneFusion(Gene('HGNC', 'TMPRSS2'), Gene('HGNC', 'ERG'), EnumeratedFusionRange('c', 1, 79), EnumeratedFusionRange('c', 312, 5034)) self.assertEqual( 'g(fus(HGNC:TMPRSS2, "c.1_79", HGNC:ERG, "c.312_5034"))', dsl.as_bel())
def test_gene_fusion_specified(self): node = GeneFusion(partner_5p=Gene(namespace='HGNC', name='TMPRSS2'), range_5p=EnumeratedFusionRange('c', 1, 79), partner_3p=Gene(namespace='HGNC', name='ERG'), range_3p=EnumeratedFusionRange('c', 312, 5034)) self.assertEqual( 'g(fus(HGNC:TMPRSS2, "c.1_79", HGNC:ERG, "c.312_5034"))', str(node))
def test_fusion(self): node_data = GeneFusion(partner_5p=Gene('HGNC', 'TMPRSS2'), partner_3p=Gene('HGNC', 'ERG'), range_5p=EnumeratedFusionRange('c', 1, 79), range_3p=EnumeratedFusionRange('c', 312, 5034)) node_data = node_data self.graph.add_node_from_data(node_data) self.assertIn(node_data, self.graph) self.assertEqual(1, self.graph.number_of_nodes()) self.assertEqual(0, self.graph.number_of_edges())
cftr = hgnc('CFTR') cftr_protein_unspecified_variant = cftr.with_variants(HgvsUnspecified()) cftr_protein_phe_508_del = cftr.with_variants(Hgvs('p.Phe508del')) adenocarcinoma = Pathology('MESHD', 'Adenocarcinoma') interleukin_23_complex = NamedComplexAbundance('GO', 'interleukin-23 complex') oxygen_atom = Abundance(namespace='CHEBI', name='oxygen atom') hydrogen_peroxide = Abundance('CHEBI', 'hydrogen peroxide') tmprss2_gene = Gene('HGNC', 'TMPRSS2') tmprss2_erg_gene_fusion = GeneFusion( partner_5p=tmprss2_gene, range_5p=EnumeratedFusionRange('c', 1, 79), partner_3p=Gene('HGNC', 'ERG'), range_3p=EnumeratedFusionRange('c', 312, 5034) ) bcr_jak2_gene_fusion = GeneFusion( partner_5p=Gene('HGNC', 'BCR'), range_5p=EnumeratedFusionRange('c', '?', 1875), partner_3p=Gene('HGNC', 'JAK2'), range_3p=EnumeratedFusionRange('c', 2626, '?') ) chchd4_aifm1_gene_fusion = GeneFusion( partner_5p=Gene('HGNC', 'CHCHD4'), partner_3p=Gene('HGNC', 'AIFM1') )
def test_fusion_unspecified(self, mock): node_data = GeneFusion( Gene('HGNC', 'TMPRSS2'), Gene('HGNC', 'ERG'), ) self._help_reconstitute(node_data, 1, 0)