Utilities¶

model_to_mat ¶

model_to_mat(model, file_name, varname=None)

Save the cobra model as a .mat file.

This .mat file can be used directly in the MATLAB version of COBRA.

Parameters:

Name	Type	Description	Default
`model`	`cobra.core.Model.Model object`	The model to save	required
`file_name`	`str or file-like object`	The file to save to	required
`varname`	`string`	The name of the variable within the workspace	`None`

load_test_model ¶

load_test_model(
    name: str = "e_coli_core.xml",
    use_gene_level: bool = True,
    model_path: Optional[PathLike] = None,
) -> cobra.Model

Get a cobra.Model in the core folder

Parameters:

Name	Type	Description	Default
`name`	`str`	file name of the cobra.Model	`'e_coli_core.xml'`
`use_gene_level`	`bool`	If true, use gene entrez id (without transcript part)	`True`
`model_path`	`Optional[PathLike]`	The path of model directory, default: ../../assets/core from the folder the package is located	`None`

Returns:

Type	Description
`Model`	The requested cobra.Model

save_model ¶

save_model(
    model: Model, output_file_name: Union[str, PathLike]
) -> None

Save a cobra.Model

Parameters:

Name	Type	Description	Default
`model`	`Model`	Saved cobra.Model	required
`output_file_name`	`Union[str, PathLike]`	Saved core' file name	required

Returns:

Type	Description
`None`

load_model ¶

load_model(model_file_path: str) -> cobra.Model

Parameters:

Name	Type	Description	Default
`model_file_path`	`str`		required

Returns:

Type	Description
`Model`

make_irrev_rxn ¶

make_irrev_rxn(
    mod,
    rxn_id,
    add_inplace=True,
    ignore_irrev=False,
    forward_prefix="_F_",
    backward_prefix="_R_",
    *,
    remove_original=False,
    copy_attributes=True
) -> List[cobra.Reaction]

Create irreversible forward/backward copies of a reaction.

A reversible reaction lb < 0 < ub is represented as two non-negative flux reactions: a forward copy with the original stoichiometry and a backward copy with negated stoichiometry. This is the representation needed for enzyme constraints because enzyme usage must be non-negative in both directions.

Parameters:

Name	Type	Description	Default
`mod`	`Model`	Model containing the reaction.	required
`rxn_id`	`str`	ID of the reaction to split.	required
`add_inplace`	`bool`	Add the generated reactions to mod.	`True`
`ignore_irrev`	`bool`	If True, skip only directions with zero feasible capacity.	`False`
`forward_prefix`	`str`	Prefixes used to generate reaction IDs.	`'_F_'`
`backward_prefix`	`str`	Prefixes used to generate reaction IDs.	`'_F_'`
`remove_original`	`bool`	If True and `add_inplace` is True, remove the original reaction after adding the irreversible copies.	`False`
`copy_attributes`	`bool`	Copy name, subsystem, GPR, notes, and annotation to generated reactions.	`True`

get_logger ¶

get_logger(name: str) -> logging.Logger

Get a logger within the pipeGEM namespace.

Parameters:

Name	Type	Description	Default
`name`	`str`	The name of the logger, typically `__name__` of the calling module.	required

Returns:

Type	Description
`Logger`