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# -*- coding: utf-8 -*-
"""Tests for node deletion functions."""
import unittest
from pybel import BELGraph
from pybel.constants import POSITIVE_CORRELATION, RELATION
from pybel.dsl import (
CompositeAbundance,
Protein,
gene,
hgvs,
pathology,
protein_fusion,
rna,
rna_fusion,
)
from pybel.struct.mutation import (
enrich_protein_and_rna_origins,
prune_protein_rna_origins,
remove_associations,
remove_isolated_list_abundances,
remove_pathologies,
)
from pybel.struct.mutation.utils import remove_isolated_nodes, remove_isolated_nodes_op
from pybel.testing.utils import n
trem2_gene = gene(namespace="HGNC", name="TREM2")
trem2_rna = rna(namespace="HGNC", name="TREM2")
trem2_protein = Protein(namespace="HGNC", name="TREM2")
class TestDeletions(unittest.TestCase):
"""Test cases for deletion functions."""
def test_remove_pathologies(self):
"""Test removal of pathologies."""
g = BELGraph()
p1, p2, p3 = (Protein(namespace="HGNC", name=n()) for _ in range(3))
d1, d2 = (pathology(namespace="MESH", name=n()) for _ in range(2))
g.add_increases(p1, p2, citation=n(), evidence=n())
g.add_increases(p2, p3, citation=n(), evidence=n())
g.add_positive_correlation(p1, d1, citation=n(), evidence=n())
g.add_positive_correlation(p2, d1, citation=n(), evidence=n())
g.add_association(p2, d1, citation=n(), evidence=n())
g.add_positive_correlation(d1, d2, citation=n(), evidence=n())
g.add_positive_correlation(d1, d2, citation=n(), evidence=n())
self.assertEqual(5, g.number_of_nodes())
self.assertEqual(12, g.number_of_edges())
self.assertEqual(2, len(g[p2][d1]))
remove_associations(g)
relations = list(g[p2][d1].values())
self.assertEqual(1, len(relations))
self.assertEqual(POSITIVE_CORRELATION, relations[0][RELATION])
self.assertEqual(5, g.number_of_nodes())
self.assertEqual(10, g.number_of_edges())
self.assertEqual(5, g.number_of_nodes())
remove_pathologies(g)
self.assertTrue(p1, g)
self.assertTrue(p2, g)
self.assertTrue(p3, g)
self.assertEqual(3, g.number_of_nodes())
self.assertEqual(2, g.number_of_edges())
def test_remove_isolated_in_place(self):
"""Test removing isolated nodes (in-place)."""
g = BELGraph()
g.add_edge(1, 2)
g.add_edge(2, 3)
g.add_node(4)
remove_isolated_nodes(g)
self.assertEqual(3, g.number_of_nodes())
self.assertEqual(2, g.number_of_edges())
def test_remove_isolated_out_of_place(self):
"""Test removing isolated nodes (out-of-place)."""
g = BELGraph()
g.add_edge(1, 2)
g.add_edge(2, 3)
g.add_node(4)
g = remove_isolated_nodes_op(g)
self.assertEqual(3, g.number_of_nodes())
self.assertEqual(2, g.number_of_edges())
def test_remove_isolated_list_abundances(self):
"""Test removing isolated list abundances."""
g = BELGraph()
p1, p2 = [Protein("HGNC", n()) for _ in range(2)]
node = CompositeAbundance([p1, p2])
g.add_node_from_data(node)
self.assertEqual(3, g.number_of_nodes())
remove_isolated_list_abundances(g)
self.assertEqual(2, g.number_of_nodes())
self.assertIn(p1, g)
self.assertIn(p2, g)
class TestProcessing(unittest.TestCase):
"""Test inference of the central dogma."""
def assert_in_graph(self, node, graph):
"""Assert the node is in the graph.
:type node: pybel.dsl.BaseEntity
:type graph: pybel.BELGraph
:rtype: bool
"""
self.assertIn(node, graph)
def assert_not_in_graph(self, node, graph):
"""Assert the node is not in the graph.
:type node: pybel.dsl.BaseEntity
:type graph: pybel.BELGraph
:rtype: bool
"""
self.assertNotIn(node, graph)
def test_infer_on_sialic_acid_example(self):
"""Test infer_central_dogma on the sialic acid example."""
graph = BELGraph()
graph.add_node_from_data(trem2_protein)
self.assert_in_graph(trem2_protein, graph)
self.assert_not_in_graph(trem2_gene, graph)
self.assert_not_in_graph(trem2_rna, graph)
enrich_protein_and_rna_origins(graph)
self.assert_in_graph(trem2_gene, graph)
self.assert_in_graph(trem2_rna, graph)
prune_protein_rna_origins(graph)
self.assert_not_in_graph(trem2_gene, graph)
self.assert_not_in_graph(trem2_rna, graph)
self.assert_in_graph(trem2_protein, graph)
def test_no_infer_on_protein_variants(self):
"""Test that expansion doesn't occur on protein variants."""
p = Protein("HGNC", n(), variants=[hgvs(n())])
graph = BELGraph()
graph.add_node_from_data(p)
self.assertEqual(2, graph.number_of_nodes())
self.assertEqual(1, graph.number_of_edges())
enrich_protein_and_rna_origins(graph)
self.assertEqual(4, graph.number_of_nodes())
self.assertEqual(3, graph.number_of_edges())
def test_no_infer_on_rna_variants(self):
"""Test that expansion doesn't occur on RNA variants."""
r = rna("HGNC", n(), variants=[hgvs(n())])
graph = BELGraph()
graph.add_node_from_data(r)
self.assertEqual(2, graph.number_of_nodes())
self.assertEqual(1, graph.number_of_edges())
enrich_protein_and_rna_origins(graph)
self.assertEqual(3, graph.number_of_nodes())
self.assertEqual(2, graph.number_of_edges())
def test_no_infer_protein_fusion(self):
"""Test that no gene is inferred from a RNA fusion node."""
partner5p = Protein(n(), n())
partner3p = Protein(n(), n())
p = protein_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_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())
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