def test_fragment_specified_end_only(self, mock): dummy_namespace = n() dummy_name = n() node_data = Protein(namespace=dummy_namespace, name=dummy_name, variants=[Fragment(start='*', stop=1000)]) self._help_reconstitute(node_data, 2, 1)
def test_fragment_unspecified(self, mock): dummy_namespace = n() dummy_name = n() node_data = Protein(namespace=dummy_namespace, name=dummy_name, variants=[Fragment()]) self._help_reconstitute(node_data, 2, 1)
def test_get_parent(self): """Test the get_parent function in :class:`CentralDogmaAbundance`s.""" ab42 = Protein(name='APP', namespace='HGNC', variants=[Fragment(start=672, stop=713)]) app = ab42.get_parent() self.assertEqual('p(HGNC:APP)', app.as_bel()) self.assertEqual('p(HGNC:APP, frag("672_713"))', ab42.as_bel())
def test_canonicalize_variant_dsl(self): """Use the __str__ functions in the DSL to create BEL instead of external pybel.canonicalize.""" self.assertEqual('var("p.Val600Glu")', str(Hgvs('p.Val600Glu'))) self.assertEqual('var("p.Val600Glu")', str(ProteinSubstitution('Val', 600, 'Glu'))) self.assertEqual('pmod(go:0006468 ! "protein phosphorylation")', str(ProteinModification('Ph'))) self.assertEqual('pmod(TEST:Ph)', str(ProteinModification('Ph', namespace='TEST'))) self.assertEqual( 'pmod(TEST:Ph, Ser)', str(ProteinModification('Ph', namespace='TEST', code='Ser'))) self.assertEqual( 'pmod(TEST:Ph, Ser, 5)', str( ProteinModification('Ph', namespace='TEST', code='Ser', position=5))) self.assertEqual( 'pmod(GO:"protein phosphorylation", Thr, 308)', str( ProteinModification(name='protein phosphorylation', namespace='GO', code='Thr', position=308))) self.assertEqual('frag("?")', str(Fragment())) self.assertEqual('frag("672_713")', str(Fragment(start=672, stop=713))) self.assertEqual('frag("?", "descr")', str(Fragment(description='descr'))) self.assertEqual( 'frag("672_713", "descr")', str(Fragment(start=672, stop=713, description='descr'))) self.assertEqual('gmod(go:0006306 ! "DNA methylation")', str(GeneModification('Me'))) self.assertEqual('gmod(TEST:Me)', str(GeneModification('Me', namespace='TEST'))) self.assertEqual( 'gmod(GO:"DNA Methylation")', str(GeneModification('DNA Methylation', namespace='GO')))
def test_variants_mapping(self): graph = BELGraph() app = Protein(HGNC, 'APP') app_fragment = app.with_variants(Fragment('1_49')) graph.add_node_from_data(app_fragment) mapped_nodes = get_mapped_nodes(graph, HGNC, {'APP'}) self.assertEqual(1, len(mapped_nodes)) self.assertIn(app, mapped_nodes) self.assertEqual({app_fragment}, mapped_nodes[app])
def test_protein_fragment(self): node = Protein(name='APP', namespace='HGNC', variants=[Fragment(start=672, stop=713)]) self.assertEqual('p(HGNC:APP, frag("672_713"))', str(node))
MicroRna('HGNC', 'MIR21', variants=Hgvs('p.Phe508del')), Protein('HGNC', 'AKT1', variants=Hgvs('p.C40*')), Protein('HGNC', 'AKT1', variants=[Hgvs('p.Ala127Tyr'), ProteinModification('Ph', 'Ser')]), chchd4_aifm1_gene_fusion, tmprss2_erg_protein_fusion, Protein('HGNC', 'AKT1', variants=Hgvs('p.Arg1851*')), bcr_jak2_protein_fusion, Protein('HGNC', 'AKT1', variants=Hgvs('p.40*')), chchd4_aifm1_protein_fusion, Protein('HGNC', 'CFTR', variants=HgvsReference()), cftr, egfr, cftr_protein_unspecified_variant, adenocarcinoma, cftr_protein_phe_508_del, Protein('HGNC', 'MIA', variants=Fragment(5, 20)), mia, interleukin_23_complex, Protein('HGNC', 'MIA', variants=Fragment(1, '?')), Protein('HGNC', 'MIA', variants=Fragment()), Protein('HGNC', 'MIA', variants=Fragment(description='55kD')), Protein('HGNC', 'CFTR', variants=Hgvs('p.Gly576Ala')), akt1_rna, Rna('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('p.Phe508del')]), Gene('HGNC', 'NCF1'), ComplexAbundance([ Gene('HGNC', 'NCF1'), Protein('HGNC', 'HBP1') ]), Protein('HGNC', 'HBP1'), ComplexAbundance([Protein('HGNC', 'FOS'), Protein('HGNC', 'JUN')]),
def test_with_variants_list(self): """Test the `with_variant` function in :class:`CentralDogmaAbundance`s.""" app = Protein(name='APP', namespace='HGNC') ab42 = app.with_variants([Fragment(start=672, stop=713)]) self.assertEqual('p(HGNC:APP)', app.as_bel()) self.assertEqual('p(HGNC:APP, frag("672_713"))', ab42.as_bel())
Gene('HGNC', 'CFTR', variants=Hgvs('c.1521_1523delCTT')), Protein('HGNC', 'AKT1', variants=ProteinModification('Ph', 'Ser', 473)), MicroRna('HGNC', 'MIR21', variants=Hgvs('p.Phe508del')), Protein('HGNC', 'AKT1', variants=Hgvs('p.C40*')), Protein('HGNC', 'AKT1', variants=[Hgvs('p.Ala127Tyr'), ProteinModification('Ph', 'Ser')]), chchd4_aifm1_gene_fusion, tmprss2_erg_protein_fusion, Protein('HGNC', 'AKT1', variants=Hgvs('p.Arg1851*')), bcr_jak2_protein_fusion, Protein('HGNC', 'AKT1', variants=Hgvs('p.40*')), chchd4_aifm1_protein_fusion, Protein('HGNC', 'CFTR', variants=HgvsReference()), cftr, egfr, cftr_protein_unspecified_variant, adenocarcinoma, cftr_protein_phe_508_del, Protein('HGNC', 'MIA', variants=Fragment(5, 20)), mia, interleukin_23_complex, Protein('HGNC', 'MIA', variants=Fragment(1, '?')), Protein('HGNC', 'MIA', variants=Fragment()), Protein('HGNC', 'MIA', variants=Fragment(description='55kD')), Protein('HGNC', 'CFTR', variants=Hgvs('p.Gly576Ala')), akt1_rna, Rna('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('p.Phe508del')]), Gene('HGNC', 'NCF1'), ComplexAbundance([Gene('HGNC', 'NCF1'), Protein('HGNC', 'HBP1')]), Protein('HGNC', 'HBP1'), ComplexAbundance([Protein('HGNC', 'FOS'), Protein('HGNC', 'JUN')]), Protein('HGNC', 'FOS'),