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_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_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_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)