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"""Test functionalities of model component modifcations."""
from cobra.core import Model
from cobra.manipulation import escape_ID, rename_genes
def test_escape_ids(model: Model) -> None:
"""Test model component IDs' SBML compliance."""
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
def test_rename_genes(model: Model) -> None:
"""Test gene renaming functionality."""
original_name = model.genes.b1241.name
rename_dict = {
"b1241": "foo",
"hello": "world",
"b3115": "b3115",
"b2465": "b3919",
"bar": "2935",
}
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")
}
def test_rename_genes_with_context(model: Model) -> None:
"""Test gene renaming functionality is reversed with context."""
original_name = model.genes.b1241.name
rename_dict = {
"b1241": "foo",
"hello": "world",
"b3115": "b3115",
"b2465": "b3919",
"bar": "2935",
}
genes_in_old_model = set()
print(model.genes.b1241.reactions)
for i in rename_dict.keys():
if i not in rename_dict.values() and i in model.genes:
genes_in_old_model.add(i)
with model:
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")
}
print(model.genes._dict)
print(model.genes)
for i in genes_in_old_model:
if i not in rename_dict.values():
assert i in model.genes
print(model.genes._dict)
print(model.genes)
assert "b3115" in model.genes
assert "foo" not in model.genes
assert "world" not in model.genes
# make sure the object name was preserved
assert model.genes.b1241.name == original_name
# make sure the reactions are correct
assert len(model.genes.b1241.reactions) == 2
assert model.reactions.ACALD.gene_reaction_rule == "b0351 or b1241"
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 b2465"
assert model.reactions.TKT1.genes == {model.genes.b2935, model.genes.b2465}
assert model.genes.b2465.reactions == {
model.reactions.get_by_id(i) for i in ("TKT1", "TKT2")
}
assert model.genes.b3919.reactions == {model.reactions.get_by_id("TPI")}
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