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"""Test functionalities of model component pruning functions."""
from itertools import chain
from cobra.core import GPR, Metabolite, Model, Reaction
from cobra.manipulation import (
knock_out_model_genes,
prune_unused_metabolites,
prune_unused_reactions,
remove_genes,
)
def test_prune_unused_metabolites_output_type(model: Model) -> None:
"""Test the output type of unused metabolites pruning."""
[model.reactions.get_by_id(x).remove_from_model() for x in ["RPI", "RPE", "GND"]]
model_pruned, unused = prune_unused_metabolites(model)
assert isinstance(model_pruned, Model)
# test that the output contains metabolite objects
assert isinstance(unused[0], Metabolite)
def test_prune_unused_metabolites_sanity(model: Model) -> None:
"""Test the sanity of unused metabolites pruning."""
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 = prune_unused_metabolites(model)
assert metabolite1 in model.metabolites
assert metabolite2 in model.metabolites
assert metabolite3 in model.metabolites
# test that the unused metabolites are not used in the model
assert metabolite1 not in model_pruned.metabolites
assert metabolite2 not in model_pruned.metabolites
assert metabolite3 not in model_pruned.metabolites
def test_prune_unused_reactions_output_type(model: Model) -> None:
"""Test the output type of unused reactions pruning."""
reaction = Reaction("foo")
model.add_reactions([reaction])
model_pruned, unused = prune_unused_reactions(model)
assert isinstance(model_pruned, Model)
# test that the output contains reaction objects
assert isinstance(unused[0], Reaction)
def test_prune_unused_rxns_functionality(model: Model) -> None:
"""Test the sanity of unused reactions pruning."""
for x in ["foo1", "foo2", "foo3"]:
model.add_reactions([Reaction(x)])
model_pruned, unused = prune_unused_reactions(model)
assert "foo1" in model.reactions
assert "foo2" in model.reactions
assert "foo3" in model.reactions
# test that the unused reactions are not used in the model
assert "foo1" not in model_pruned.reactions
assert "foo2" not in model_pruned.reactions
assert "foo3" not in model_pruned.reactions
def test_gene_knockout(salmonella: Model) -> None:
"""Test gene knockout with and without context."""
gene_list = ["STM1067", "STM0227"]
dependent_reactions = [
"3HAD100",
"3HAD120",
"3HAD121",
"3HAD140",
"3HAD141",
"3HAD160",
"3HAD161",
"3HAD180",
"3HAD181",
"3HAD40",
"3HAD60",
"3HAD80",
"T2DECAI",
]
orig_gene_len = len(salmonella.genes)
orig_bounds = salmonella.reactions.list_attr("bounds")
with salmonella:
expected_reactions = [
salmonella.reactions.get_by_id(r) for r in dependent_reactions
]
knocked_out_reactions = knock_out_model_genes(salmonella, gene_list)
assert set(expected_reactions) == set(knocked_out_reactions)
assert len(salmonella.genes) == orig_gene_len
assert salmonella.reactions.list_attr("bounds") == orig_bounds
with salmonella:
expected_reactions = [salmonella.reactions.get_by_id("PGI")]
knocked_out_reactions = knock_out_model_genes(salmonella, ["STM4221"])
assert expected_reactions == knocked_out_reactions
with salmonella:
expected_reactions = [salmonella.reactions.get_by_id("PGI")]
knocked_out_reactions = knock_out_model_genes(
salmonella, [salmonella.genes.get_by_id("STM4221")]
)
assert expected_reactions == knocked_out_reactions
with salmonella:
expected_reactions = [salmonella.reactions.get_by_id("PGI")]
knocked_out_reactions = knock_out_model_genes(
salmonella, [salmonella.genes.index("STM4221")]
)
assert expected_reactions == knocked_out_reactions
with salmonella:
expected_reactions = [salmonella.reactions.get_by_id("4PEPTabcpp")]
knocked_out_reactions = knock_out_model_genes(salmonella, ["STM1746.S"])
assert expected_reactions == knocked_out_reactions
knocked_out_reactions = knock_out_model_genes(salmonella, gene_list)
assert len(knocked_out_reactions) == 13
expected_reactions = [
salmonella.reactions.get_by_id(r) for r in dependent_reactions
]
assert set(knocked_out_reactions) == set(expected_reactions)
knocked_out_reactions.extend(knock_out_model_genes(salmonella, ["STM4221"]))
expected_reactions.append(salmonella.reactions.get_by_id("PGI"))
assert set(knocked_out_reactions) == set(expected_reactions)
# 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_reactions([test_reaction_1])
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["eggs"])
assert knocked_out_reactions == list()
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["eggs", "spam"])
expected_reactions = [test_model.reactions.get_by_id("test1")]
assert set(knocked_out_reactions) == set(expected_reactions)
# test computation with nested boolean expression
test_reaction_1.gene_reaction_rule = "g1 and g2 and (g3 or g4 or (g5 and g6))"
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g3"])
assert knocked_out_reactions == list()
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g1"])
assert knocked_out_reactions == [test_reaction_1]
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g5"])
assert knocked_out_reactions == list()
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g3", "g4", "g5"])
assert knocked_out_reactions == [test_reaction_1]
# test computation when gene names are python expressions
test_reaction_1.gene_reaction_rule = "g1 and (for or in)"
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["for", "in"])
assert knocked_out_reactions == [test_reaction_1]
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["for"])
assert knocked_out_reactions == list()
test_reaction_1.gene_reaction_rule = "g1 and g2 and g2.conjugate"
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g2"])
assert knocked_out_reactions == [test_reaction_1]
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["g2.conjugate"])
assert knocked_out_reactions == [test_reaction_1]
test_reaction_1.gene_reaction_rule = "g1 and (try:' or 'except:1)"
with test_model:
knocked_out_reactions = knock_out_model_genes(test_model, ["try:'"])
assert knocked_out_reactions == []
with test_model:
knocked_out_reactions = knock_out_model_genes(
test_model, ["try:'", "'except:1"]
)
assert knocked_out_reactions == [test_reaction_1]
def test_remove_genes() -> None:
"""Test gene removal."""
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 == ""
def test_remove_genes_with_context() -> None:
"""Test gene removal is reversed in context."""
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 = ""
with m:
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 == ""
assert "a" in m.genes
assert "x" in m.genes
assert rxns.r1.gene_reaction_rule == "(a and b) or (c and a)"
assert rxns.r2.gpr == GPR.from_string("(a and b and d and e)")
assert rxns.r3.gene_reaction_rule == "(a and b) or (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 == ""
with m:
remove_genes(m, ["a"], remove_reactions=False)
assert "a" not in m.genes
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 == ""
assert "a" in m.genes
assert "x" in m.genes
assert len(m.reactions) == 8
assert rxns.r1.gene_reaction_rule == "(a and b) or (c and a)"
assert rxns.r2.gpr == GPR.from_string("(a and b and d and e)")
assert rxns.r3.gene_reaction_rule == "(a and b) or (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 == ""
|
