cobra.flux_analysis.deletion ============================ .. py:module:: cobra.flux_analysis.deletion .. autoapi-nested-parse:: Provide functions for reaction and gene deletions. Attributes ---------- .. autoapisummary:: cobra.flux_analysis.deletion.configuration Classes ------- .. autoapisummary:: cobra.flux_analysis.deletion.KnockoutAccessor Functions --------- .. autoapisummary:: cobra.flux_analysis.deletion._get_growth cobra.flux_analysis.deletion._reaction_deletion cobra.flux_analysis.deletion._reaction_deletion_worker cobra.flux_analysis.deletion._gene_deletion cobra.flux_analysis.deletion._gene_deletion_worker cobra.flux_analysis.deletion._init_worker cobra.flux_analysis.deletion._multi_deletion cobra.flux_analysis.deletion._entities_ids cobra.flux_analysis.deletion._element_lists cobra.flux_analysis.deletion.single_reaction_deletion cobra.flux_analysis.deletion.single_gene_deletion cobra.flux_analysis.deletion.double_reaction_deletion cobra.flux_analysis.deletion.double_gene_deletion Module Contents --------------- .. py:data:: configuration .. py:function:: _get_growth(model: cobra.core.Model) -> Tuple[float, str] Return the growth from the `model`. :param model: The model to obtain growth for. :type model: cobra.Model :returns: The obtained growth value. Returns nan if there is some error while optimizing. :rtype: float .. py:function:: _reaction_deletion(model: cobra.core.Model, reaction_ids: List[str]) -> Tuple[List[str], float, str] Perform reaction deletion. :param model: The model to perform reaction deletion on. :type model: cobra.Model :param ids: The reaction IDs to knock-out. :type ids: list of str :returns: A tuple containing reaction IDs knocked out, growth of the model and the solver status. :rtype: tuple of (list of str, float, str) .. py:function:: _reaction_deletion_worker(ids: List[str]) -> Tuple[List[str], float, str] Perform reaction deletions on worker process. :param ids: The reaction IDs to knock-out. :type ids: list of str :returns: A tuple containing reaction IDs knocked out, growth of the model and the solver status. :rtype: tuple of (list of str, float, str) .. py:function:: _gene_deletion(model: cobra.core.Model, gene_ids: List[str]) -> Tuple[List[str], float, str] Perform gene deletions. :param model: The model to perform gene deletion on. :type model: cobra.Model :param ids: The gene IDs to knock-out. :type ids: list of str :returns: A tuple containing gene IDs knocked out, growth of the model and the solver status. :rtype: tuple of (list of str, float, str) .. py:function:: _gene_deletion_worker(ids: List[str]) -> Tuple[List[str], float, str] Perform gene deletions on worker process. :param ids: The gene IDs to knock-out. :type ids: list of str :returns: A tuple containing gene IDs knocked out, growth of the model and the solver status. :rtype: tuple of (list of str, float, str) .. py:function:: _init_worker(model: cobra.core.Model) -> None Initialize worker process. .. py:function:: _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. :param model: The metabolic model to perform deletions in. :type model: cobra.Model :param entity: The entity to knockout. :type entity: {"gene", "reaction"} :param element_lists: List of cobra.Gene or cobra.Reaction to be deleted. :type element_lists: list of cobra.Gene or cobra.Reaction :param method: Method used to predict the growth rate (default "fba"). :type method: {"fba", "moma", "linear moma", "room", "linear room"}, optional :param solution: A previous solution to use as a reference for (linear) MOMA or ROOM (default None). :type solution: cobra.Solution, optional :param processes: 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). :type processes: int, optional :param \*\*kwargs: Passed on to underlying simulation functions. :returns: A representation of all combinations of entity deletions. The columns are 'growth' and 'status', where index : tuple(str) The gene or reaction identifiers that were knocked out. growth : float The growth rate of the adjusted model. status : str The solution's status. :rtype: pandas.DataFrame .. py:function:: _entities_ids(entities: List[Union[str, cobra.core.Gene, cobra.core.Reaction]]) -> List[str] Return the IDs of the `entities`. :param entities: The list of entities whose IDs need to be returned. :type entities: list of str or cobra.Gene or cobra.Reaction :returns: The IDs of the `entities`. :rtype: list of str .. py:function:: _element_lists(entities: List[Union[str, cobra.core.Gene, cobra.core.Reaction]], *ids: List[str]) -> List[str] Return the elements. :param entities: The list of entities. :type entities: list of str or cobra.Gene or cobra.Reaction :param \*ids: The list of IDs. :type \*ids: list of str :returns: The list of IDs. :rtype: list of str .. py:function:: 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`. :param model: The metabolic model to perform deletions in. :type model: cobra.Model :param reaction_list: The reactions be knocked out. If not passed, all the reactions from the model are used (default None). :type reaction_list: list of cobra.Reaction or str, optional :param method: Method used to predict the growth rate (default "fba"). :type method: {"fba", "moma", "linear moma", "room", "linear room"}, optional :param solution: A previous solution to use as a reference for (linear) MOMA or ROOM (default None). :type solution: cobra.Solution, optional :param processes: 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). :type processes: int, optional :param \*\*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 index : tuple(str) The reaction identifier that was knocked out. growth : float The growth rate of the adjusted model. status : str The solution's status. :rtype: pandas.DataFrame .. py:function:: 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`. :param model: The metabolic model to perform deletions in. :type model: cobra.Model :param gene_list: The gene objects to be deleted. If not passed, all the genes from the model are used (default None). :type gene_list: list of cobra.Gene or str, optional :param method: Method used to predict the growth rate (default "fba"). :type method: {"fba", "moma", "linear moma", "room", "linear room"}, optional :param solution: A previous solution to use as a reference for (linear) MOMA or ROOM (default None). :type solution: cobra.Solution, optional :param processes: 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). :type processes: int, optional :param \*\*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 index : tuple(str) The gene identifier that was knocked out. growth : float The growth rate of the adjusted model. status : str The solution's status. :rtype: pandas.DataFrame .. py:function:: 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. :param model: The metabolic model to perform deletions in. :type model: cobra.Model :param reaction_list1: The first reaction list to be deleted. If not passed, all the reactions from the model are used (default None). :type reaction_list1: list of cobra.Reaction or str, optional :param reaction_list2: The second reaction list to be deleted. If not passed, all the reactions from the model are used (default None). :type reaction_list2: list of cobra.Reaction or str, optional :param method: Method used to predict the growth rate (default "fba"). :type method: {"fba", "moma", "linear moma", "room", "linear room"}, optional :param solution: A previous solution to use as a reference for (linear) MOMA or ROOM (default None). :type solution: cobra.Solution, optional :param processes: 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). :type processes: int, optional :param \*\*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 index : tuple(str) The reaction identifiers that were knocked out. growth : float The growth rate of the adjusted model. status : str The solution's status. :rtype: pandas.DataFrame .. py:function:: 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. :param model: The metabolic model to perform deletions in. :type model: cobra.Model :param gene_list1: The first gene list to be deleted. If not passed, all the genes from the model are used (default None). :type gene_list1: list of cobra.Gene or str, optional :param gene_list2: The second gene list to be deleted. If not passed, all the genes from the model are used (default None). :type gene_list2: list of cobra.Gene or str, optional :param method: Method used to predict the growth rate (default None). :type method: {"fba", "moma", "linear moma", "room", "linear room"}, optional :param solution: A previous solution to use as a reference for (linear) MOMA or ROOM (default None). :type solution: cobra.Solution, optional :param processes: 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). :type processes: int, optional :param \*\*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 index : tuple(str) The gene identifiers that were knocked out. growth : float The growth rate of the adjusted model. status : str The solution's status. :rtype: pandas.DataFrame .. py:class:: 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_obj : pandas.DataFrame or pandas.Series A result from one of the deletion methods. .. py:attribute:: _result .. py:method:: _validate(obj: pandas.DataFrame) -> None :staticmethod: Validate the object given. :param obj: The object to validate. :type obj: pandas.DataFrame :raises AttributeError: If the object supplied is not a DataFrame. .. py:method:: __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. :param args: 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. :type args: cobra.Reaction, cobra.Gene, str, set, or list :returns: The deletion result where the chosen entities have been deleted. Each row denotes a deletion. :rtype: pandas.DataFrame :raises ValueError: If any other object is used as index for lookup.