# -*- coding: utf-8 -*-
from __future__ import absolute_import
from itertools import chain
import pytest
from cobra.core import Metabolite, Model, Reaction
from cobra.manipulation import *
[docs]class TestManipulation:
"""Test functions in cobra.manipulation"""
[docs] def test_escape_ids(self, model):
model.reactions.PGI.gene_reaction_rule = "a.b or c"
assert "a.b" in model.genes
escape_ID(model)
assert "a.b" not in model.genes
[docs] def test_rename_gene(self, model):
original_name = model.genes.b1241.name
rename_dict = {
"b1241": "foo",
"hello": "world",
"b3115": "b3115",
"b2465": "b3919",
"bar": "2935",
}
modify.rename_genes(model, rename_dict)
for i in rename_dict.keys():
if i not in rename_dict.values():
assert i not in model.genes
assert "b3115" in model.genes
assert "foo" in model.genes
assert "world" not in model.genes
# make sure the object name was preserved
assert model.genes.foo.name == original_name
# make sure the reactions are correct
assert len(model.genes.foo.reactions) == 2
assert model.reactions.ACALD.gene_reaction_rule == "b0351 or foo"
assert model.reactions.TPI.gene_reaction_rule == "b3919"
assert model.reactions.TPI.genes == {model.genes.b3919}
assert model.reactions.TKT1.gene_reaction_rule == "b2935 or b3919"
assert model.reactions.TKT1.genes == {model.genes.b2935, model.genes.b3919}
assert model.genes.b3919.reactions == {
model.reactions.get_by_id(i) for i in ("TKT1", "TKT2", "TPI")
}
[docs] def test_gene_knockout_computation(self, salmonella):
def find_gene_knockout_reactions_fast(cobra_model, gene_list):
compiled_rules = get_compiled_gene_reaction_rules(cobra_model)
return find_gene_knockout_reactions(
cobra_model, gene_list, compiled_gene_reaction_rules=compiled_rules
)
def get_removed(m):
return {x.id for x in m._trimmed_reactions}
def test_computation(m, gene_ids, expected_reaction_ids):
genes = [m.genes.get_by_id(i) for i in gene_ids]
expected_reactions = {
m.reactions.get_by_id(i) for i in expected_reaction_ids
}
removed1 = set(find_gene_knockout_reactions(m, genes))
removed2 = set(find_gene_knockout_reactions_fast(m, genes))
assert removed1 == expected_reactions
assert removed2 == expected_reactions
delete_model_genes(m, gene_ids, cumulative_deletions=False)
assert get_removed(m) == expected_reaction_ids
undelete_model_genes(m)
gene_list = ["STM1067", "STM0227"]
dependent_reactions = {
"3HAD121",
"3HAD160",
"3HAD80",
"3HAD140",
"3HAD180",
"3HAD100",
"3HAD181",
"3HAD120",
"3HAD60",
"3HAD141",
"3HAD161",
"T2DECAI",
"3HAD40",
}
test_computation(salmonella, gene_list, dependent_reactions)
test_computation(salmonella, ["STM4221"], {"PGI"})
test_computation(salmonella, ["STM1746.S"], {"4PEPTabcpp"})
# test cumulative behavior
delete_model_genes(salmonella, gene_list[:1])
delete_model_genes(salmonella, gene_list[1:], cumulative_deletions=True)
delete_model_genes(salmonella, ["STM4221"], cumulative_deletions=True)
dependent_reactions.add("PGI")
assert get_removed(salmonella) == dependent_reactions
# non-cumulative following cumulative
delete_model_genes(salmonella, ["STM4221"], cumulative_deletions=False)
assert get_removed(salmonella) == {"PGI"}
# make sure on reset that the bounds are correct
reset_bound = salmonella.reactions.get_by_id("T2DECAI").upper_bound
assert reset_bound == 1000.0
# test computation when gene name is a subset of another
test_model = Model()
test_reaction_1 = Reaction("test1")
test_reaction_1.gene_reaction_rule = "eggs or (spam and eggspam)"
test_model.add_reaction(test_reaction_1)
test_computation(test_model, ["eggs"], set())
test_computation(test_model, ["eggs", "spam"], {"test1"})
# test computation with nested boolean expression
test_reaction_1.gene_reaction_rule = "g1 and g2 and (g3 or g4 or (g5 and g6))"
test_computation(test_model, ["g3"], set())
test_computation(test_model, ["g1"], {"test1"})
test_computation(test_model, ["g5"], set())
test_computation(test_model, ["g3", "g4", "g5"], {"test1"})
# test computation when gene names are python expressions
test_reaction_1.gene_reaction_rule = "g1 and (for or in)"
test_computation(test_model, ["for", "in"], {"test1"})
test_computation(test_model, ["for"], set())
test_reaction_1.gene_reaction_rule = "g1 and g2 and g2.conjugate"
test_computation(test_model, ["g2"], {"test1"})
test_computation(test_model, ["g2.conjugate"], {"test1"})
test_reaction_1.gene_reaction_rule = "g1 and (try:' or 'except:1)"
test_computation(test_model, ["try:'"], set())
test_computation(test_model, ["try:'", "'except:1"], {"test1"})
[docs] def test_remove_genes(self):
m = Model("test")
m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)])
assert len(m.reactions) == 8
rxns = m.reactions
rxns.r1.gene_reaction_rule = "(a and b) or (c and a)"
rxns.r2.gene_reaction_rule = "(a and b and d and e)"
rxns.r3.gene_reaction_rule = "(a and b) or (b and c)"
rxns.r4.gene_reaction_rule = "(f and b) or (b and c)"
rxns.r5.gene_reaction_rule = "x"
rxns.r6.gene_reaction_rule = "y"
rxns.r7.gene_reaction_rule = "x or z"
rxns.r8.gene_reaction_rule = ""
assert "a" in m.genes
assert "x" in m.genes
remove_genes(m, ["a"], remove_reactions=False)
assert "a" not in m.genes
assert "x" in m.genes
assert rxns.r1.gene_reaction_rule == ""
assert rxns.r2.gene_reaction_rule == ""
assert rxns.r3.gene_reaction_rule == "b and c"
assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)"
assert rxns.r5.gene_reaction_rule == "x"
assert rxns.r6.gene_reaction_rule == "y"
assert rxns.r7.genes == {m.genes.x, m.genes.z}
assert rxns.r8.gene_reaction_rule == ""
remove_genes(m, ["x"], remove_reactions=True)
assert len(m.reactions) == 7
assert "r5" not in m.reactions
assert "x" not in m.genes
assert rxns.r1.gene_reaction_rule == ""
assert rxns.r2.gene_reaction_rule == ""
assert rxns.r3.gene_reaction_rule == "b and c"
assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)"
assert rxns.r6.gene_reaction_rule == "y"
assert rxns.r7.gene_reaction_rule == "z"
assert rxns.r7.genes == {m.genes.z}
assert rxns.r8.gene_reaction_rule == ""
[docs] def test_sbo_annotation(self, model):
rxns = model.reactions
rxns.EX_o2_e.annotation.clear()
fake_DM = Reaction("DM_h_c")
model.add_reaction(fake_DM)
fake_DM.add_metabolites({model.metabolites.get_by_id("h_c"): -1})
# this exchange will be set wrong. The function should not overwrite
# an existing SBO annotation
rxns.get_by_id("EX_h_e").annotation["sbo"] = "SBO:0000628"
add_SBO(model)
assert rxns.EX_o2_e.annotation["sbo"] == "SBO:0000627"
assert rxns.DM_h_c.annotation["sbo"] == "SBO:0000628"
assert rxns.EX_h_e.annotation["sbo"] == "SBO:0000628"
[docs] def test_validate_mass_balance(self, model):
assert len(check_mass_balance(model)) == 0
# if we remove the SBO term which marks the reaction as
# mass balanced, then the reaction should be detected as
# no longer mass balanced
EX_rxn = model.reactions.query(lambda r: r.boundary)[0]
EX_rxn.annotation.pop("sbo")
balance = check_mass_balance(model)
assert len(balance) == 1
assert EX_rxn in balance
m1 = Metabolite("m1", formula="()")
r1 = Reaction("r1")
r1.add_metabolites({m1: 1})
with pytest.raises(ValueError), pytest.warns(UserWarning):
r1.check_mass_balance()
[docs] def test_prune_unused_mets_output_type(self, model):
# test that the output contains metabolite objects
metabolite = model.metabolites.ru5p__D_c
[
model.reactions.get_by_id(x).remove_from_model()
for x in ["RPI", "RPE", "GND"]
]
model_pruned, unused = delete.prune_unused_metabolites(model)
assert isinstance(model_pruned, Model)
assert isinstance(unused[0], Metabolite)
[docs] def test_prune_unused_mets_functionality(self, model):
# test that the unused metabolites are not used in the model
metabolite1 = model.metabolites.ru5p__D_c
metabolite2 = model.metabolites.akg_e
metabolite3 = model.metabolites.akg_c
reactions = set(
chain(metabolite1.reactions, metabolite2.reactions, metabolite3.reactions)
)
model.remove_reactions(reactions)
model_pruned, unused = delete.prune_unused_metabolites(model)
assert metabolite1 in model.metabolites
assert metabolite2 in model.metabolites
assert metabolite3 in model.metabolites
assert metabolite1 not in model_pruned.metabolites
assert metabolite2 not in model_pruned.metabolites
assert metabolite3 not in model_pruned.metabolites
[docs] def test_prune_unused_rxns_output_type(self, model):
# test that the output contains reaction objects
reaction = Reaction("foo")
model.add_reaction(reaction)
model_pruned, unused = delete.prune_unused_reactions(model)
assert isinstance(model_pruned, Model)
assert isinstance(unused[0], Reaction)
[docs] def test_prune_unused_rxns_functionality(self, model):
# test that the unused reactions are not used in the model
for x in ["foo1", "foo2", "foo3"]:
model.add_reaction(Reaction(x))
model_pruned, unused = delete.prune_unused_reactions(model)
assert "foo1" in model.reactions
assert "foo2" in model.reactions
assert "foo3" in model.reactions
assert "foo1" not in model_pruned.reactions
assert "foo2" not in model_pruned.reactions
assert "foo3" not in model_pruned.reactions