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# -*- coding: utf-8 -*-
"""Tests for collapse functions."""
import unittest
from pybel import BELGraph
from pybel.constants import DIRECTLY_INCREASES
from pybel.dsl import gene, mirna, pathology, pmod, protein, rna
from pybel.struct.mutation.collapse import (
collapse_all_variants,
collapse_nodes,
collapse_to_genes,
surviors_are_inconsistent,
)
from pybel.testing.utils import n
HGNC = "HGNC"
GO = "GO"
CHEBI = "CHEBI"
g1 = gene(HGNC, "1")
r1 = rna(HGNC, "1")
p1 = protein(HGNC, "1")
p1_phosphorylated = protein(HGNC, "1", variants=[pmod("Ph")])
g2 = gene(HGNC, "2")
r2 = rna(HGNC, "2")
p2 = protein(HGNC, "2")
g3 = gene(HGNC, "3")
r3 = rna(HGNC, "3")
p3 = protein(HGNC, "3")
g4 = gene(HGNC, "4")
m4 = mirna(HGNC, "4")
p5 = pathology(GO, "5")
class TestCollapse(unittest.TestCase):
"""Tests for collapse functions."""
def test_check_survivors_consistent(self):
"""Test the survivor mapping is consistent."""
inconsistencies = surviors_are_inconsistent(
{
1: {2},
3: {4},
}
)
self.assertEqual(0, len(inconsistencies))
self.assertFalse(inconsistencies)
inconsistencies = surviors_are_inconsistent(
{
1: {2},
2: {3},
3: {4},
5: {4},
}
)
self.assertEqual(2, len(inconsistencies))
self.assertIn(2, inconsistencies)
self.assertIn(3, inconsistencies)
def test_collapse_by_dict(self):
"""Test collapsing nodes by a dictionary."""
graph = BELGraph()
graph.add_node_from_data(p1)
graph.add_node_from_data(p2)
graph.add_node_from_data(p3)
graph.add_increases(p1, p3, citation=n(), evidence=n())
graph.add_qualified_edge(p2, p3, relation=DIRECTLY_INCREASES, citation=n(), evidence=n())
self.assertEqual(3, graph.number_of_nodes())
self.assertEqual(2, graph.number_of_edges())
d = {p1: {p2}}
collapse_nodes(graph, d)
self.assertEqual({p1, p3}, set(graph))
self.assertEqual({(p1, p3), (p1, p3)}, set(graph.edges()))
self.assertEqual(2, graph.number_of_edges(), msg=graph.edges(data=True, keys=True))
def test_collapse_dogma_1(self):
"""Test collapsing to genes, only with translations."""
graph = BELGraph()
graph.add_translation(r1, p1)
self.assertEqual(2, graph.number_of_nodes())
self.assertEqual(1, graph.number_of_edges())
collapse_to_genes(graph)
self.assertIn(g1, graph)
self.assertEqual(1, graph.number_of_nodes())
self.assertEqual(0, graph.number_of_edges())
def test_collapse_dogma_2(self):
"""Test collapsing to genes with translations and transcriptions."""
graph = BELGraph()
graph.add_transcription(g1, r1)
graph.add_translation(r1, p1)
self.assertEqual(3, graph.number_of_nodes())
self.assertEqual(2, graph.number_of_edges())
collapse_to_genes(graph)
self.assertIn(g1, graph)
self.assertEqual(1, graph.number_of_nodes())
self.assertEqual(0, graph.number_of_edges())
def test_collapse_dogma_3(self):
"""Test collapsing to genes, only with transcriptions."""
graph = BELGraph()
graph.add_transcription(g1, r1)
self.assertEqual(2, graph.number_of_nodes())
self.assertEqual(1, graph.number_of_edges())
collapse_to_genes(graph)
self.assertIn(g1, graph)
self.assertEqual(1, graph.number_of_nodes())
self.assertEqual(0, graph.number_of_edges())
def test_collapse_all_variants(self):
"""Test collapsing all variants to their reference nodes."""
graph = BELGraph()
graph.add_node_from_data(p1_phosphorylated)
graph.add_increases(p1_phosphorylated, p2, citation=n(), evidence=n())
self.assertEqual(3, graph.number_of_nodes())
self.assertEqual(2, graph.number_of_edges())
collapse_all_variants(graph)
self.assertEqual(2, graph.number_of_nodes())
self.assertEqual(1, graph.number_of_edges())
self.assertIn(p1, graph)
self.assertNotIn(p1_phosphorylated, graph)
self.assertIn(p2, graph)
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