def test_rna_fusion_specified(self):
node = rna_fusion(partner_5p=rna(namespace='HGNC', name='TMPRSS2'),
range_5p=fusion_range('r', 1, 79),
partner_3p=rna(namespace='HGNC', name='ERG'),
range_3p=fusion_range('r', 312, 5034))
self.assertEqual(
'r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034"))',
str(node))
def test_no_infer_rna_fusion(self):
"""Test that no RNA nor gene is inferred from a protein fusion node."""
partner5p = rna(n(), n())
partner3p = rna(n(), n())
p = rna_fusion(partner_3p=partner3p, partner_5p=partner5p)
graph = BELGraph()
graph.add_node_from_data(p)
self.assertEqual(1, graph.number_of_nodes())
self.assertEqual(0, graph.number_of_edges())
enrich_protein_and_rna_origins(graph)
self.assertEqual(1, graph.number_of_nodes())
self.assertEqual(0, graph.number_of_edges())
def test_rna_fusion_unspecified(self):
node = rna_fusion(
partner_5p=rna(namespace='HGNC', name='TMPRSS2'),
partner_3p=rna(namespace='HGNC', name='ERG'),
)
self.assertEqual('r(fus(HGNC:TMPRSS2, "?", HGNC:ERG, "?"))', str(node))