def test_gene_fusion_missing_implicit(self):
"""Test serialization of a gene fusion to BEL with a implicit missing fusion ranges."""
dsl = gene_fusion(
gene('HGNC', 'TMPRSS2'),
gene('HGNC', 'ERG'),
)
self.assertEqual('g(fus(HGNC:TMPRSS2, "?", HGNC:ERG, "?"))', dsl.as_bel())
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_gene_fusion_specified(self):
node = gene_fusion(partner_5p=gene(namespace='HGNC', name='TMPRSS2'),
range_5p=fusion_range('c', 1, 79),
partner_3p=gene(namespace='HGNC', name='ERG'),
range_3p=fusion_range('c', 312, 5034))
self.assertEqual(
'g(fus(HGNC:TMPRSS2, "c.1_79", HGNC:ERG, "c.312_5034"))',
str(node))