"""Provide functions to modify model components."""
from ast import NodeTransformer
from itertools import chain
from typing import TYPE_CHECKING, Dict
from ..core.gene import ast2str
from .delete import get_compiled_gene_reaction_rules
if TYPE_CHECKING:
from cobra import Gene, Model
# Set of tuples of operators and their corresponding textual form
[docs]_renames = (
(".", "_DOT_"),
("(", "_LPAREN_"),
(")", "_RPAREN_"),
("-", "__"),
("[", "_LSQBKT"),
("]", "_RSQBKT"),
(",", "_COMMA_"),
(":", "_COLON_"),
(">", "_GT_"),
("<", "_LT"),
("/", "_FLASH"),
("\\", "_BSLASH"),
("+", "_PLUS_"),
("=", "_EQ_"),
(" ", "_SPACE_"),
("'", "_SQUOT_"),
('"', "_DQUOT_"),
)
[docs]def _escape_str_id(id_str: str) -> str:
"""Make a single string ID SBML compliant.
Parameters
----------
id_str: str
The ID string to operate on.
Returns
-------
str
The SBML compliant ID string.
"""
for c in ("'", '"'):
if id_str.startswith(c) and id_str.endswith(c) and id_str.count(c) == 2:
id_str = id_str.strip(c)
for char, escaped_char in _renames:
id_str = id_str.replace(char, escaped_char)
return id_str
[docs]class _GeneEscaper(NodeTransformer):
"""Class to represent a gene ID escaper."""
[docs] def visit_Name(self, node: "Gene") -> "Gene":
"""Escape string ID.
Parameters
----------
node: cobra.Gene
The gene object to work on.
Returns
-------
cobra.Gene
The gene object whose ID has been escaped.
"""
node.id = _escape_str_id(node.id)
return node
[docs]def escape_ID(model: "Model") -> None:
"""Make all model component object IDs SBML compliant.
Parameters
----------
model: cobra.Model
The model to operate on.
"""
for x in chain([model], model.metabolites, model.reactions, model.genes):
x.id = _escape_str_id(x.id)
model.repair()
gene_renamer = _GeneEscaper()
for rxn, rule in get_compiled_gene_reaction_rules(model).items():
if rule is not None:
rxn._gene_reaction_rule = ast2str(gene_renamer.visit(rule))
[docs]class _Renamer(NodeTransformer):
"""
Class to represent a gene renamer.
Parameters
----------
rename_dict: dict of {str: str}
The dictionary having keys as old gene names
and value as new gene names.
"""
def __init__(self, rename_dict: Dict[str, str], **kwargs) -> None:
"""Initialize a new object.
Other Parameters
----------------
**kwargs:
Further keyword arguments are passed on to the parent class.
"""
super().__init__(**kwargs)
self.rename_dict = rename_dict
[docs] def visit_Name(self, node: "Gene") -> "Gene":
"""Rename a gene.
Parameters
----------
node: cobra.Gene
The gene to rename.
Returns
-------
cobra.Gene
The renamed gene object.
"""
node.id = self.rename_dict.get(node.id, node.id)
return node
[docs]def rename_genes(model: "Model", rename_dict: Dict[str, str]) -> None:
"""Rename genes in a model from the `rename_dict`.
Parameters
----------
model: cobra.Model
The model to operate on.
rename_dict: dict of {str: str}
The dictionary having keys as old gene names
and value as new gene names.
"""
recompute_reactions = set() # need to recompute related genes
remove_genes = []
for old_name, new_name in rename_dict.items():
# undefined if there a value matches a different key
try:
gene_index = model.genes.index(old_name)
except ValueError:
gene_index = None
old_gene_present = gene_index is not None
new_gene_present = new_name in model.genes
if old_gene_present and new_gene_present:
old_gene = model.genes.get_by_id(old_name)
# Added in case not renaming some genes:
if old_gene is not model.genes.get_by_id(new_name):
remove_genes.append(old_gene)
recompute_reactions.update(old_gene._reaction)
elif old_gene_present and not new_gene_present:
# rename old gene to new gene
gene = model.genes[gene_index]
# trick DictList into updating index
model.genes._dict.pop(gene.id) # ugh
gene.id = new_name
model.genes[gene_index] = gene
elif not old_gene_present and new_gene_present:
pass
else: # if not old gene_present and not new_gene_present
# the new gene's _model will be set by repair
# This would add genes from rename_dict
# that are not associated with a rxn
# cobra_model.genes.append(Gene(new_name))
pass
model.repair()
gene_renamer = _Renamer(rename_dict)
for rxn, rule in get_compiled_gene_reaction_rules(model).items():
if rule is not None:
rxn._gene_reaction_rule = ast2str(gene_renamer.visit(rule))
for rxn in recompute_reactions:
rxn.gene_reaction_rule = rxn._gene_reaction_rule
for i in remove_genes:
model.genes.remove(i)