def find_gene_knockout_reactions(cobra_model,
gene_list,
compiled_gene_reaction_rules=None):
"""identify reactions which will be disabled when the genes are knocked out
cobra_model: :class:`~cobra.core.Model.Model`
gene_list: iterable of :class:`~cobra.core.Gene.Gene`
compiled_gene_reaction_rules: dict of {reaction_id: compiled_string}
If provided, this gives pre-compiled gene_reaction_rule strings.
The compiled rule strings can be evaluated much faster. If a rule
is not provided, the regular expression evaluation will be used.
Because not all gene_reaction_rule strings can be evaluated, this
dict must exclude any rules which can not be used with eval.
"""
potential_reactions = set()
for gene in gene_list:
if isinstance(gene, string_types):
gene = cobra_model.genes.get_by_id(gene)
potential_reactions.update(gene._reaction)
gene_set = {str(i) for i in gene_list}
if compiled_gene_reaction_rules is None:
compiled_gene_reaction_rules = {
r: parse_gpr(r.gene_reaction_rule)[0]
for r in potential_reactions
}
return [
r for r in potential_reactions
if not eval_gpr(compiled_gene_reaction_rules[r], gene_set)
]
def remove_genes(cobra_model, gene_list, remove_reactions=True):
"""remove genes entirely from the model
This will also simplify all gene_reaction_rules with this
gene inactivated."""
gene_set = {cobra_model.genes.get_by_id(str(i)) for i in gene_list}
gene_id_set = {i.id for i in gene_set}
remover = _GeneRemover(gene_id_set)
ast_rules = get_compiled_gene_reaction_rules(cobra_model)
target_reactions = []
for reaction, rule in iteritems(ast_rules):
if reaction.gene_reaction_rule is None or \
len(reaction.gene_reaction_rule) == 0:
continue
# reactions to remove
if remove_reactions and not eval_gpr(rule, gene_id_set):
target_reactions.append(reaction)
else:
# if the reaction is not removed, remove the gene
# from its gpr
remover.visit(rule)
new_rule = ast2str(rule)
if new_rule != reaction.gene_reaction_rule:
reaction.gene_reaction_rule = new_rule
for gene in gene_set:
cobra_model.genes.remove(gene)
cobra_model.remove_reactions(target_reactions)
def find_gene_knockout_reactions(cobra_model, gene_list,
compiled_gene_reaction_rules=None):
"""identify reactions which will be disabled when the genes are knocked out
cobra_model: :class:`~cobra.core.Model.Model`
gene_list: iterable of :class:`~cobra.core.Gene.Gene`
compiled_gene_reaction_rules: dict of {reaction_id: compiled_string}
If provided, this gives pre-compiled gene_reaction_rule strings.
The compiled rule strings can be evaluated much faster. If a rule
is not provided, the regular expression evaluation will be used.
Because not all gene_reaction_rule strings can be evaluated, this
dict must exclude any rules which can not be used with eval.
"""
potential_reactions = set()
for gene in gene_list:
if isinstance(gene, string_types):
gene = cobra_model.genes.get_by_id(gene)
potential_reactions.update(gene._reaction)
gene_set = {str(i) for i in gene_list}
if compiled_gene_reaction_rules is None:
compiled_gene_reaction_rules = {r: parse_gpr(r.gene_reaction_rule)[0]
for r in potential_reactions}
return [r for r in potential_reactions
if not eval_gpr(compiled_gene_reaction_rules[r], gene_set)]
def remove_genes(cobra_model, gene_list, remove_reactions=True):
"""remove genes entirely from the model
This will also simplify all gene_reaction_rules with this
gene inactivated."""
gene_set = {cobra_model.genes.get_by_id(str(i)) for i in gene_list}
gene_id_set = {i.id for i in gene_set}
remover = _GeneRemover(gene_id_set)
ast_rules = get_compiled_gene_reaction_rules(cobra_model)
target_reactions = []
for reaction, rule in iteritems(ast_rules):
if reaction.gene_reaction_rule is None or \
len(reaction.gene_reaction_rule) == 0:
continue
# reactions to remove
if remove_reactions and not eval_gpr(rule, gene_id_set):
target_reactions.append(reaction)
else:
# if the reaction is not removed, remove the gene
# from its gpr
remover.visit(rule)
new_rule = ast2str(rule)
if new_rule != reaction.gene_reaction_rule:
reaction.gene_reaction_rule = new_rule
for gene in gene_set:
cobra_model.genes.remove(gene)
# remove reference to the gene in all groups
associated_groups = cobra_model.get_associated_groups(gene)
for group in associated_groups:
group.remove_members(gene)
cobra_model.remove_reactions(target_reactions)
def functional(self):
"""All required enzymes for reaction are functional.
Returns
-------
bool
True if the gene-protein-reaction (GPR) rule is fulfilled for
this reaction, or if reaction is not associated to a model,
otherwise False.
"""
if self._model:
tree, _ = parse_gpr(self.gene_reaction_rule)
return eval_gpr(tree, {gene.id for gene in self.genes if
not gene.functional})
return True
def functional(self):
"""All required enzymes for reaction are functional.
Returns
-------
bool
True if the gene-protein-reaction (GPR) rule is fulfilled for
this reaction, or if reaction is not associated to a model,
otherwise False.
"""
if self._model:
tree, _ = parse_gpr(self.gene_reaction_rule)
return eval_gpr(tree, {gene.id for gene in self.genes if
not gene.functional})
return True