Source code for cobra.test.test_manipulation.test_modify

"""Test functionalities of model component modifcations."""

from cobra.core import Model
from cobra.manipulation import escape_ID, rename_genes

[docs]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
[docs]def test_rename_genes(model: Model) -> None: """Test gene renaming functionality.""" original_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 == original_name # make sure the reactions are correct assert len( == 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")