def test_gene_fusion(self):
"""Test serialization of a gene fusion to BEL with a explicit fusion ranges."""
dsl = gene_fusion(gene('HGNC', 'TMPRSS2'), gene('HGNC', 'ERG'),
fusion_range('c', 1, 79),
fusion_range('c', 312, 5034))
self.assertEqual(
'g(fus(HGNC:TMPRSS2, "c.1_79", HGNC:ERG, "c.312_5034"))',
dsl.as_bel())
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_names_fusions(self):
"""Test that names inside fusions are still found by the iterator."""
graph = BELGraph()
graph.namespace_url['HGNC'] = 'http://dummy'
node = protein_fusion(partner_5p=protein(name='A', namespace='HGNC'),
range_5p=fusion_range('p', 1, 15),
partner_3p=protein(name='B', namespace='HGNC'),
range_3p=fusion_range('p', 1, 100))
graph.add_node_from_data(node)
result = {
'A': 1,
'B': 1,
}
self.assertEqual(set(result), get_names_by_namespace(graph, 'HGNC'))
self.assertEqual(result, count_names_by_namespace(graph, 'HGNC'))
def test_canonicalize_fusion_range_dsl(self):
"""Test canonicalization of enumerated fusion ranges."""
self.assertEqual('p.1_15', str(fusion_range('p', 1, 15)))
self.assertEqual('p.*_15', str(fusion_range('p', '*', 15)))