cobra.flux_analysis.deletion

Provide functions for reaction and gene deletions.

Module Contents

Classes

KnockoutAccessor

Access unique combinations of reactions in deletion results.

Functions

_get_growth(→ Tuple[float, str])	Return the growth from the model.
_reaction_deletion(→ Tuple[List[str], float, str])	Perform reaction deletion.
_reaction_deletion_worker(→ Tuple[List[str], float, str])	Perform reaction deletions on worker process.
_gene_deletion(→ Tuple[List[str], float, str])	Perform gene deletions.
_gene_deletion_worker(→ Tuple[List[str], float, str])	Perform gene deletions on worker process.
_init_worker(→ None)	Initialize worker process.
_multi_deletion(→ pandas.DataFrame)	Provide a common interface for single or multiple knockouts.
_entities_ids(→ List[str])	Return the IDs of the entities.
_element_lists(→ List[str])	Return the elements.
single_reaction_deletion(→ pandas.DataFrame)	Knock out each reaction from reaction_list.
single_gene_deletion(→ pandas.DataFrame)	Knock out each gene from gene_list.
double_reaction_deletion(→ pandas.DataFrame)	Knock out each reaction pair from the combinations of two given lists.
double_gene_deletion(→ pandas.DataFrame)	Knock out each gene pair from the combination of two given lists.

Attributes

configuration

cobra.flux_analysis.deletion.configuration

cobra.flux_analysis.deletion._get_growth(model: cobra.core.Model) → Tuple[float, str]

Return the growth from the model.

Parameters

model (cobra.Model) – The model to obtain growth for.

Returns

The obtained growth value. Returns nan if there is some error while optimizing.

Return type

float

cobra.flux_analysis.deletion._reaction_deletion(model: cobra.core.Model, reaction_ids: List[str]) → Tuple[List[str], float, str]

Perform reaction deletion.

Parameters

• model (cobra.Model) – The model to perform reaction deletion on.

• ids (list of str) – The reaction IDs to knock-out.

Returns

A tuple containing reaction IDs knocked out, growth of the model and the solver status.

Return type

tuple of (list of str, float, str)

cobra.flux_analysis.deletion._reaction_deletion_worker(ids: List[str]) → Tuple[List[str], float, str]

Perform reaction deletions on worker process.

Parameters

ids (list of str) – The reaction IDs to knock-out.

Returns

A tuple containing reaction IDs knocked out, growth of the model and the solver status.

Return type

tuple of (list of str, float, str)

cobra.flux_analysis.deletion._gene_deletion(model: cobra.core.Model, gene_ids: List[str]) → Tuple[List[str], float, str]

Perform gene deletions.

Parameters

• model (cobra.Model) – The model to perform gene deletion on.

• ids (list of str) – The gene IDs to knock-out.

Returns

A tuple containing gene IDs knocked out, growth of the model and the solver status.

Return type

tuple of (list of str, float, str)

cobra.flux_analysis.deletion._gene_deletion_worker(ids: List[str]) → Tuple[List[str], float, str]

Perform gene deletions on worker process.

Parameters

ids (list of str) – The gene IDs to knock-out.

Returns

A tuple containing gene IDs knocked out, growth of the model and the solver status.

Return type

tuple of (list of str, float, str)

cobra.flux_analysis.deletion._init_worker(model: cobra.core.Model) → None

Initialize worker process.

cobra.flux_analysis.deletion._multi_deletion(model: cobra.core.Model, entity: str, element_lists: List[Union[cobra.core.Gene, cobra.core.Reaction]], method: str = 'fba', solution: Optional[cobra.Solution] = None, processes: Optional[int] = None, **kwargs) → pandas.DataFrame

Provide a common interface for single or multiple knockouts.

Parameters

• model (cobra.Model) – The metabolic model to perform deletions in.

• entity ({"gene", "reaction"}) – The entity to knockout.

• element_lists (list of cobra.Gene or cobra.Reaction) – List of cobra.Gene or cobra.Reaction to be deleted.

• method ({"fba", "moma", "linear moma", "room", "linear room"}, optional) – Method used to predict the growth rate (default “fba”).

• solution (cobra.Solution, optional) – A previous solution to use as a reference for (linear) MOMA or ROOM (default None).

• processes (int, optional) – The number of parallel processes to run. Can speed up the computations if the number of knockouts to perform is large. If not passed, will be set to configuration.processes (default None).

• **kwargs – Passed on to underlying simulation functions.

Returns

A representation of all combinations of entity deletions. The columns are ‘growth’ and ‘status’, where

indextuple(str)

The gene or reaction identifiers that were knocked out.

growthfloat

The growth rate of the adjusted model.

statusstr

The solution’s status.

Return type

pandas.DataFrame

cobra.flux_analysis.deletion._entities_ids(entities: List[Union[str, cobra.core.Gene, cobra.core.Reaction]]) → List[str]

Return the IDs of the entities.

Parameters

entities (list of str or cobra.Gene or cobra.Reaction) – The list of entities whose IDs need to be returned.

Returns

The IDs of the entities.

Return type

list of str

cobra.flux_analysis.deletion._element_lists(entities: List[Union[str, cobra.core.Gene, cobra.core.Reaction]], *ids: List[str]) → List[str]

Return the elements.

Parameters

• entities (list of str or cobra.Gene or cobra.Reaction) – The list of entities.

• *ids (list of str) – The list of IDs.

Returns

The list of IDs.

Return type

list of str

cobra.flux_analysis.deletion.single_reaction_deletion(model: cobra.core.Model, reaction_list: Optional[List[Union[cobra.core.Reaction, str]]] = None, method: str = 'fba', solution: Optional[cobra.Solution] = None, processes: Optional[int] = None, **kwargs) → pandas.DataFrame

Knock out each reaction from reaction_list.

Parameters

• model (cobra.Model) – The metabolic model to perform deletions in.

• reaction_list (list of cobra.Reaction or str, optional) – The reactions be knocked out. If not passed, all the reactions from the model are used (default None).

• method ({"fba", "moma", "linear moma", "room", "linear room"}, optional) – Method used to predict the growth rate (default “fba”).

• solution (cobra.Solution, optional) – A previous solution to use as a reference for (linear) MOMA or ROOM (default None).

• processes (int, optional) – The number of parallel processes to run. Can speed up the computations if the number of knockouts to perform is large. If not passed, will be set to configuration.processes (default None).

• **kwargs – Keyword arguments are passed on to underlying simulation functions such as add_room.

Returns

A representation of all single reaction deletions. The columns are ‘growth’ and ‘status’, where

indextuple(str)

The reaction identifier that was knocked out.

growthfloat

The growth rate of the adjusted model.

statusstr

The solution’s status.

Return type

pandas.DataFrame

cobra.flux_analysis.deletion.single_gene_deletion(model: cobra.core.Model, gene_list: Optional[List[Union[cobra.core.Gene, str]]] = None, method: str = 'fba', solution: Optional[cobra.Solution] = None, processes: Optional[int] = None, **kwargs) → pandas.DataFrame

Knock out each gene from gene_list.

Parameters

• model (cobra.Model) – The metabolic model to perform deletions in.

• gene_list (list of cobra.Gene or str, optional) – The gene objects to be deleted. If not passed, all the genes from the model are used (default None).

• method ({"fba", "moma", "linear moma", "room", "linear room"}, optional) – Method used to predict the growth rate (default “fba”).

• solution (cobra.Solution, optional) – A previous solution to use as a reference for (linear) MOMA or ROOM (default None).

• processes (int, optional) – The number of parallel processes to run. Can speed up the computations if the number of knockouts to perform is large. If not passed, will be set to configuration.processes (default None).

• **kwargs – Keyword arguments are passed on to underlying simulation functions such as add_room.

Returns

A representation of all single gene deletions. The columns are ‘growth’ and ‘status’, where

indextuple(str)

The gene identifier that was knocked out.

growthfloat

The growth rate of the adjusted model.

statusstr

The solution’s status.

Return type

pandas.DataFrame

cobra.flux_analysis.deletion.double_reaction_deletion(model: cobra.core.Model, reaction_list1: Optional[List[Union[cobra.core.Reaction, str]]] = None, reaction_list2: Optional[List[Union[cobra.core.Reaction, str]]] = None, method: str = 'fba', solution: Optional[cobra.Solution] = None, processes: Optional[int] = None, **kwargs) → pandas.DataFrame

Knock out each reaction pair from the combinations of two given lists.

We say ‘pair’ here but the order order does not matter.

Parameters

• model (cobra.Model) – The metabolic model to perform deletions in.

• reaction_list1 (list of cobra.Reaction or str, optional) – The first reaction list to be deleted. If not passed, all the reactions from the model are used (default None).

• reaction_list2 (list of cobra.Reaction or str, optional) – The second reaction list to be deleted. If not passed, all the reactions from the model are used (default None).

• method ({"fba", "moma", "linear moma", "room", "linear room"}, optional) – Method used to predict the growth rate (default “fba”).

• solution (cobra.Solution, optional) – A previous solution to use as a reference for (linear) MOMA or ROOM (default None).

• processes (int, optional) – The number of parallel processes to run. Can speed up the computations if the number of knockouts to perform is large. If not passed, will be set to configuration.processes (default None).

• **kwargs – Keyword arguments are passed on to underlying simulation functions such as add_room.

Returns

A representation of all combinations of reaction deletions. The columns are ‘growth’ and ‘status’, where

indextuple(str)

The reaction identifiers that were knocked out.

growthfloat

The growth rate of the adjusted model.

statusstr

The solution’s status.

Return type

pandas.DataFrame

cobra.flux_analysis.deletion.double_gene_deletion(model: cobra.core.Model, gene_list1: Optional[List[Union[cobra.core.Gene, str]]] = None, gene_list2: Optional[List[Union[cobra.core.Gene, str]]] = None, method: str = 'fba', solution: Optional[cobra.Solution] = None, processes: Optional[int] = None, **kwargs) → pandas.DataFrame

Knock out each gene pair from the combination of two given lists.

We say ‘pair’ here but the order order does not matter.

Parameters

• model (cobra.Model) – The metabolic model to perform deletions in.

• gene_list1 (list of cobra.Gene or str, optional) – The first gene list to be deleted. If not passed, all the genes from the model are used (default None).

• gene_list2 (list of cobra.Gene or str, optional) – The second gene list to be deleted. If not passed, all the genes from the model are used (default None).

• method ({"fba", "moma", "linear moma", "room", "linear room"}, optional) – Method used to predict the growth rate (default None).

• solution (cobra.Solution, optional) – A previous solution to use as a reference for (linear) MOMA or ROOM (default None).

• processes (int, optional) – The number of parallel processes to run. Can speed up the computations if the number of knockouts to perform is large. If not passed, will be set to configuration.processes (default None).

• **kwargs – Keyword arguments are passed on to underlying simulation functions such as add_room.

Returns

A representation of all combinations of gene deletions. The columns are ‘growth’ and ‘status’, where

indextuple(str)

The gene identifiers that were knocked out.

growthfloat

The growth rate of the adjusted model.

statusstr

The solution’s status.

Return type

pandas.DataFrame

class cobra.flux_analysis.deletion.KnockoutAccessor(pandas_obj: Union[pandas.DataFrame, pandas.Series])

Access unique combinations of reactions in deletion results.

This allows acces in the form of results.knockout[rxn1] or results.knockout[“rxn1_id”]. Each individual entry will return a deletion so results.knockout[rxn1, rxn2] will return two deletions (for individual knockouts of rxn1 and rxn2 respectively). Multi-deletions can be accessed by passing in sets like results.knockout[{rxn1, rxn2}] which denotes the double deletion of both reactions. Thus, the following are allowed index elements:

• single reactions or genes (depending on whether it is a gene or reaction deletion)

• single reaction IDs or gene IDs

• lists of single single reaction IDs or gene IDs (will return one row for each element in the list)

• sets of reactions or genes (for multi-deletions)

• sets of reactions IDs or gene IDs

• list of sets of objects or IDs (to get several multi-deletions)

Parameters:

pandas_objpandas.DataFrame or pandas.Series

A result from one of the deletion methods.

static _validate(obj: pandas.DataFrame) → None

Validate the object given.

Parameters

obj (pandas.DataFrame) – The object to validate.

Raises

AttributeError – If the object supplied is not a DataFrame.

__getitem__(args: Union[cobra.core.Gene, List[cobra.core.Gene], Set[cobra.core.Gene], List[Set[cobra.core.Gene]], cobra.core.Reaction, List[cobra.core.Reaction], Set[cobra.core.Reaction], List[Set[cobra.core.Reaction]], str, List[str], Set[str], List[Set[str]]]) → pandas.DataFrame

Return the deletion result for a particular set of knocked entities.

Parameters

args (cobra.Reaction, cobra.Gene, str, set, or list) – The deletions to be returned. Accepts: - single reactions or genes - single reaction IDs or gene IDs - lists of single single reaction IDs or gene IDs - sets of reactions or genes - sets of reactions IDs or gene IDs - list of sets of objects or IDs See the docs for usage examples.

Returns

The deletion result where the chosen entities have been deleted. Each row denotes a deletion.

Return type

pandas.DataFrame

Raises

ValueError – If any other object is used as index for lookup.