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# -*- coding: utf-8 -*-
"""Tests for expansion functions."""
import unittest
from pybel import BELGraph
from pybel.examples.sialic_acid_example import (
cd33,
cd33_phosphorylated,
shp1,
shp2,
sialic_acid,
sialic_acid_cd33_complex,
sialic_acid_graph,
syk,
)
from pybel.struct.mutation.expansion.neighborhood import (
expand_node_neighborhood,
expand_node_predecessors,
expand_node_successors,
expand_nodes_neighborhoods,
)
class TestExpansion(unittest.TestCase):
"""Test expansion functions."""
def test_neighborhood(self):
"""Test expansion around the neighborhood of CD33 in the sialic acid graph given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
self.assertEqual(1, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_neighborhood(graph=graph, universe=_sialic_acid_graph, node=cd33)
self.assertEqual(
{cd33, sialic_acid, sialic_acid_cd33_complex, cd33_phosphorylated},
set(graph),
)
def test_neighborhood_with_predecessors(self):
"""Test expansion on the predecessors of a given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(sialic_acid_cd33_complex)
self.assertEqual(3, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_predecessors(universe=_sialic_acid_graph, graph=graph, node=cd33)
self.assertEqual(4, graph.number_of_nodes())
self.assertIn(sialic_acid, graph)
self.assertIn(sialic_acid_cd33_complex, graph)
self.assertIn(cd33_phosphorylated, graph)
def test_neighborhood_with_successors(self):
"""Test expansion on the successors of a given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(cd33_phosphorylated)
self.assertEqual(2, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_successors(universe=_sialic_acid_graph, graph=graph, node=cd33)
self.assertEqual(
{sialic_acid_cd33_complex, sialic_acid, cd33_phosphorylated, cd33},
set(graph),
)
def test_neighborhoods(self):
"""Test expansion on the neighborhood of given nodes.
The edge between PTPN6/CD33ph should not be added.
"""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(syk)
self.assertEqual(2, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_nodes_neighborhoods(universe=_sialic_acid_graph, graph=graph, nodes=[cd33, syk])
self.assertNotIn(shp1, graph[cd33_phosphorylated])
self.assertNotIn(shp2, graph[cd33_phosphorylated])
self.assertEqual(
9,
graph.number_of_nodes(),
msg="wrong number of nodes: {}".format(list(graph)),
)
self.assertEqual(8, graph.number_of_edges(), msg="wrong number of edges")
self.assertIn(sialic_acid, graph)
self.assertIn(sialic_acid_cd33_complex, graph)
self.assertIn(cd33_phosphorylated, graph)
# TODO test that if new nodes with metadata that's missing (namespace_url definition, etc) then that gets added too
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