Research documentation

Use Cases

Technical Documentation

Version

Network

RESOURCE

Typing name : RESOURCE.gws_gena.Network

Brick : gws_gena

Parent :

Resource

Metabolic network

Class that represents a network.

A network is a collection of reconstructed metabolic pathways.

Views

NETWORK

Default view

JSON VIEW

SUMMARY

REACTION TABLE

COMPOUND DISTRIBUTION

REACTION GAPS

Functions

__INIT__

Constructor, please do not overwrite this method, use the init method instead Leave the constructor without parameters.

ADD_COMPOUND

Adds a compound

Parameters:

Name	Type	Default value	Description
comp	`Compound`		The compound to add `gena.network.`

ADD_REACTION

Adds a product

Parameters:

Name	Type	Default value	Description
rxn	`Reaction`		The reaction to add `gena.network.`

ADD_SIMULATION

Adds a simulation

Parameters:

Name	Type	Default value	Description
sim	`SimulationDict`		The simulation dictionary ``,

ADD_TECHNICAL_INFO

Add technical information on the resource. Technical info are useful to set additional information on the resource.

Parameters:

Name	Type	Default value	Description
technical_info	`TechnicalInfo`		Technical information to add (key, value)

CHECK_RESOURCE

You can redefine this method to define custom logic to check this resource. If there is a problem with the resource, return a string that define the error, otherwise return None This method is called on output resources of a task. If there is an error returned, the task will be set to error and next proceses will not be run. It is also call when uploading a resource (usually for files or folder), if there is an error returned, the resource will not be uploaded

Return type:

Union[str, NoneType]

CLONE

Clone the resource to create a new instance with a new id. It copies the RFields.

Return type:

ResourceType

COMPOUND_EXISTS

Check that a compound exists in the network

Parameters:

Name	Type	Default value	Description
comp	`Compound`

Return type:

bool

COPY

Returns a deep copy

Return type:

Network

CREATE_INPUT_STOICHIOMETRIC_MATRIX

Create the input stoichiometric matrix of the network

We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the consumed compounds

Parameters:

Name	Type	Default value	Description
include_biomass	`bool`	True
ignore_cofactors	`bool`	False

Return type:

DataFrame

CREATE_NON_STEADY_STOICHIOMETRIC_MATRIX

Create the non-steady stoichiometric matrix of the network

We define by non-steady stoichiometric matrix, the submatrix of the stoichimetric matrix involving the non-steady compounds (e.g. extra-cellular, biomass compounds)

Parameters:

Name	Type	Default value	Description
include_biomass	`bool`	True
ignore_cofactors	`bool`	False

Return type:

DataFrame

CREATE_OUTPUT_STOICHIOMETRIC_MATRIX

Create the output stoichiometric matrix of the network

We define by input stoichiometric matrix, the submatrix of the stoichimetric matrix involving the excreted compounds

Parameters:

Name	Type	Default value	Description
include_biomass	`bool`	True
ignore_cofactors	`bool`	False

Return type:

DataFrame

CREATE_STEADY_STOICHIOMETRIC_MATRIX

Create the steady stoichiometric matrix of the network

We define by steady stoichiometric matrix, the submatrix of the stoichimetric matrix involving the steady compounds (e.g. intra-cellular compounds)

Parameters:

Name	Type	Default value	Description
ignore_cofactors	`bool`	False

Return type:

DataFrame

CREATE_STOICHIOMETRIC_MATRIX

Create the full stoichiometric matrix of the network

Return type:

DataFrame

DUMPS

Dumps the network

Parameters:

Name	Type	Default value	Description
refresh_layout	`bool`	False

Return type:

NetworkDict

FLATTEN_COMPARTMENT_ID

Flatten the id of a compartment

Parameters:

Name	Type	Default value	Description
compartment	`Compartment`

Return type:

str

FLATTEN_COMPOUND_ID

Flatten the id of a compound

Parameters:

Name	Type	Default value	Description
comp	`Compound`

Return type:

str

FLATTEN_REACTION_ID

Flatten the id of a reaction

Parameters:

Name	Type	Default value	Description
rxn	`Reaction`

Return type:

str

GET_BIOMASS_COMPOUND

Get the biomass compounds if it exists

Return type:

Compound

GET_BIOMASS_REACTION

Get the biomass reaction if it exists

Return type:

Reaction

GET_COMPOUND_BY_ID

Get a compound by its id.

Parameters:

Name	Type	Default value	Description
comp_id	`str`		The compound id ``

Return type:

Compound

GET_COMPOUND_IDS

Get all compound ids

Return type:

List

GET_COMPOUND_STATS_AS_JSON

Get compound stats as JSON

Return type:

dict

GET_COMPOUND_STATS_AS_TABLE

Get compound stats as table

Return type:

Table

GET_COMPOUNDS_BY_CHEBI_ID

Get a compound by its chebi id and compartment.

Parameters:

Name	Type	Default value	Description
chebi_id	`str`		The chebi id of the compound ``
compartment	`Union[str, NoneType]`	None	The compartment of the compound `str`

Return type:

List

GET_COMPOUNDS_BY_COMPARTMENTS

Get the compounds in a compartments

Parameters:

Name	Type	Default value	Description
compartment_list	`List`	None

Return type:

Dict

GET_DEFAULT_NAME

You can redefine this method to set a name of the resource. When saving the resource the name will be saved automatically This can be useful to distinguish this resource from another one or to search for the resource

Return type:

str

GET_NON_STEADY_COMPOUNDS

Get the non-steady compounds

Parameters:

Name	Type	Default value	Description
ignore_cofactors	`bool`	False

Return type:

Dict

GET_NUMBER_OF_COMPOUNDS

Get number of compounds

Return type:

int

GET_NUMBER_OF_REACTIONS

Get number of reactions

Return type:

int

GET_REACTION_BOUNDS

Get the reaction bounds [lb, ub]

Return type:

DataFrame

GET_REACTION_BY_EC_NUMBER

Get a reaction by its ec number.

Parameters:

Name	Type	Default value	Description
ec_number	`str`		The ec number of the reaction ``

Return type:

Reaction

GET_REACTION_BY_ID

Get a reaction by its id.

Parameters:

Name	Type	Default value	Description
rxn_id	`str`		The reaction id ``

Return type:

Reaction

GET_REACTION_BY_RHEA_ID

Get a reaction by its rhea id.

Parameters:

Name	Type	Default value	Description
rhea_id	`str`		The rhea id of the reaction ``

Return type:

Reaction

GET_REACTION_IDS

Get all reaction ids

Return type:

List

GET_REACTIONS_RELATED_TO_CHEBI_ID

Get the reactions related to a compound with having a given CheBI ID

Parameters:

Name	Type	Default value	Description
chebi_id	`str`

Return type:

List

GET_STATS

Gather and return networks stats

Return type:

dict

GET_STATS_AS_JSON

Get stats as JSON

Return type:

dict

GET_STEADY_COMPOUNDS

Get the steady compounds

Parameters:

Name	Type	Default value	Description
ignore_cofactors	`bool`	False

Return type:

Dict

GET_SUMMARY

Return the summary of the network

Return type:

dict

GET_TECHNICAL_INFO

Get the technical information of the resource

Parameters:

Name	Type	Default value	Description
key	`str`		Key of the technical information

Return type:

TechnicalInfo

GET_TOTAL_ABS_FLUX_AS_TABLE

Get the total absolute flux as table

Return type:

Table

HAS_SINK

Return True if the network has sink reaction, False otherwise

Return type:

bool

INIT

This can be overwritten to perform custom initialization of the resource. This method is called just after the init (constructor) of the resource. The default values of RFields are set before this method is called.

MERGE

Merge with another network

Parameters:

Name	Type	Default value	Description
network	`Network`
inplace	`bool`	False

REACTION_EXISTS

Check that a reaction exists in the network

Parameters:

Name	Type	Default value	Description
rxn	`Reaction`		The reaction `gws.gena.`

Return type:

bool

REMOVE_COMPOUND

Remove a compound from the network

Parameters:

Name	Type	Default value	Description
comp_id	`str`		The id of the compound to remove ``

REMOVE_REACTION

Remove a reaction from the network

Parameters:

Name	Type	Default value	Description
rxn_id	`str`		The id of the reaction to remove ``

SET_SIMULATIONS

Set simulations

Parameters:

Name	Type	Default value	Description
simulations	`Dict`

TO_CSV

Returns a CSV representation of the network

Return type:

str

TO_DATAFRAME

Returns a DataFrame representation of the network

Return type:

DataFrame

TO_STR

Returns a string representation of the network

Return type:

str

TO_TABLE

Returns a Table representation of the network

Return type:

Table

UPDATE_COMPOUND_RECON_TAG

Set a compound recon tag

Parameters:

Name	Type	Default value	Description
tag_id	`Any`
tag_data	`dict`

UPDATE_EC_RECON_TAG

Set a ec recon tag

Parameters:

Name	Type	Default value	Description
tag_id	`Any`
tag_data	`dict`

UPDATE_REACTION_RECON_TAG

Set a reaction recon tag

Parameters:

Name	Type	Default value	Description
tag_id	`Any`
tag_data	`dict`

VIEW_AS_JSON

View as json

Parameters:

Name	Type	Default value	Description
params	`ConfigParams`

Return type:

JSONView

VIEW_AS_TABLE

View as table

Parameters:

Name	Type	Default value	Description
_	`ConfigParams`

Return type:

TableView

VIEW_COMPOUND_STATS_AS_TABLE

View compound stats as table

Parameters:

Name	Type	Default value	Description
_	`ConfigParams`

Return type:

TableView

VIEW_GAPS_AS_TABLE

View gaps as table

Parameters:

Name	Type	Default value	Description
_	`ConfigParams`

Return type:

TableView

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