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FUSION_STOP: 1875,
},
RANGE_3P: {
FUSION_REFERENCE: 'p',
FUSION_START: 2626,
FUSION_STOP: '?',
},
},
}
self.assertEqual(expected_dict, result.asDict())
expected_node = protein_fusion(
protein('HGNC', 'BCR'),
protein('HGNC', 'JAK2'),
fusion_range('p', '?', 1875),
fusion_range('p', 2626, '?')
)
self.assert_has_node(expected_node)
canonical_bel = self.graph.node_to_bel(expected_node)
self.assertEqual('p(fus(HGNC:BCR, "p.?_1875", HGNC:JAK2, "p.2626_?"))', canonical_bel)
FUSION_STOP: 1875,
},
RANGE_3P: {
FUSION_REFERENCE: 'r',
FUSION_START: 2626,
FUSION_STOP: '?',
},
},
}
self.assertEqual(expected_dict, result.asDict())
expected_node = rna_fusion(
rna('HGNC', 'BCR'),
rna('HGNC', 'JAK2'),
fusion_range('r', '?', 1875),
fusion_range('r', 2626, '?'),
)
self.assert_has_node(expected_node)
self.assertEqual('r(fus(HGNC:BCR, "r.?_1875", HGNC:JAK2, "r.2626_?"))', self.graph.node_to_bel(expected_node))
FUSION_START: 1,
FUSION_STOP: 79,
},
RANGE_3P: {
FUSION_REFERENCE: 'p',
FUSION_START: 312,
FUSION_STOP: 5034,
},
},
}
self.assertEqual(expected_dict, result.asDict())
expected_node = protein_fusion(
protein('HGNC', 'TMPRSS2'),
protein('HGNC', 'ERG'),
fusion_range('p', 1, 79),
fusion_range('p', 312, 5034),
)
self.assert_has_node(expected_node)
self.assertEqual(
'p(fus(HGNC:TMPRSS2, "p.1_79", HGNC:ERG, "p.312_5034"))',
self.graph.node_to_bel(expected_node),
)
FUSION_REFERENCE: 'c',
FUSION_START: '?',
FUSION_STOP: 1875
},
RANGE_3P: {
FUSION_REFERENCE: 'c',
FUSION_START: 2626,
FUSION_STOP: '?'
}
}
}
self.assertEqual(expected_dict, result.asDict())
expected_node = gene_fusion(gene('HGNC', 'BCR'), gene('HGNC', 'JAK2'), fusion_range('c', '?', 1875),
fusion_range('c', 2626, '?'))
self.assert_has_node(expected_node)
self.assertEqual('g(fus(HGNC:BCR, "c.?_1875", HGNC:JAK2, "c.2626_?"))', self.graph.node_to_bel(expected_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'))
RANGE_5P: {
FUSION_REFERENCE: 'c',
FUSION_START: 1,
FUSION_STOP: '?'
},
RANGE_3P: {
FUSION_REFERENCE: 'c',
FUSION_START: 312,
FUSION_STOP: 5034
}
}
}
self.assertEqual(expected_dict, result.asDict())
expected_node = gene_fusion(gene('HGNC', 'TMPRSS2'), gene('HGNC', 'ERG'), fusion_range('c', 1, '?'),
fusion_range('c', 312, 5034))
self.assert_has_node(expected_node)
canonical_bel = self.graph.node_to_bel(expected_node)
self.assertEqual('g(fus(HGNC:TMPRSS2, "c.1_?", HGNC:ERG, "c.312_5034"))', canonical_bel)
FUSION_REFERENCE: 'c',
FUSION_START: 1,
FUSION_STOP: '?'
},
RANGE_3P: {
FUSION_REFERENCE: 'c',
FUSION_START: 312,
FUSION_STOP: 5034
}
}
}
self.assertEqual(expected_dict, result.asDict())
expected_node = gene_fusion(gene('HGNC', 'TMPRSS2'), gene('HGNC', 'ERG'), fusion_range('c', 1, '?'),
fusion_range('c', 312, 5034))
self.assert_has_node(expected_node)
canonical_bel = self.graph.node_to_bel(expected_node)
self.assertEqual('g(fus(HGNC:TMPRSS2, "c.1_?", HGNC:ERG, "c.312_5034"))', canonical_bel)
FUSION_START: '?',
FUSION_STOP: 1875,
},
RANGE_3P: {
FUSION_REFERENCE: 'r',
FUSION_START: 2626,
FUSION_STOP: '?',
},
},
}
self.assertEqual(expected_dict, result.asDict())
expected_node = rna_fusion(
rna('HGNC', 'BCR'),
rna('HGNC', 'JAK2'),
fusion_range('r', '?', 1875),
fusion_range('r', 2626, '?'),
)
self.assert_has_node(expected_node)
self.assertEqual('r(fus(HGNC:BCR, "r.?_1875", HGNC:JAK2, "r.2626_?"))', self.graph.node_to_bel(expected_node))