rbatools.rba_simulation_data API documentation

rbatools.rba_simulation_data module

Classes

class SimulationDataRBA

Class holding information on simulations with the model. Attributes

StructuralInformation : rbatools.rba_model_structure.ModelStructureRBA object.
Model description
SessionName : str
Name of simulation session

ProteinData : rbatools.data_block DataBlock object. Simulated protein levels ReactionData : rbatools.data_block DataBlock object. Simulated reaction data EnzymeData : rbatools.data_block DataBlock object. Simulated enzyme data ProcessData : rbatools.data_block DataBlock object. Simulated process machinery data MetaboliteConstraintData : rbatools.data_block DataBlock object. Simulation information on mass-balance constraints DensityConstraintData : rbatools.data_block DataBlock object. Simulation information on compartment-density constraints ProcessConstraintData : rbatools.data_block DataBlock object. Simulation information on process-capacity constraints EnzymeConstraintData : rbatools.data_block DataBlock object. Simulation information on enzyme-efficiency constraints

Methods

def __init__(self, rbaModelStructure)

Initiates Simulation data object Parameters

rbaModelStructure : ModelStructureRBA
 
def export_csv(self, output_directory='', deleteZerosRows=True, return_result=False)

Exports simulation data as csv files Parameters

output_directory : str
Path to location, where csvs should be stored. Default: "" –> current directory is used
deleteZerosRows : bool
Boolean wheter to remove rows which have only zero entries. (e.g. reactions which never carry flux in all runs) Default: True
return_result : bool
Whether result should be returned. If false nothing is returned. Default: False

Returns

Dictionaries with csvs

def export_escher_map(self, type='fluxes', output_directory='', return_result=False)

Exports input file for generation of Escher maps. https://escher.github.io If argument type is 'fluxes' the method return an Eschermap for the visualisation of reaction-fluxes If argument type is 'investment' the method return an Eschermap for the visualisation of the amount of amino-acids invested in enzyme machinery for reactions.

Parameters

type : str ('fluxes' or 'investment')
Default: 'fluxes'
output_directory : str
Path to location, where csvs should be stored. Default: "" –> current directory is used
return_result : bool
Whether result should be returned. If false nothing is returned. Default: False

Returns

JSON file

def export_json(self, return_result=False)

Returns simulation data as JSON string Parameters

return_result : bool
Whether result should be returned. If false nothing is returned. Default: False

Returns

JSON string

def export_proteo_map(self, type='genes', output_directory='', return_result=False)

Exports input file for the generation of Proteo maps from simulation data. If argument type is 'proto' the method exports a proteo map with location independent protein IDs. If argument type is 'isoforms' the method exports a proteo map with location specific protein IDs. https://www.proteomaps.net

Parameters

type : str ('genes' or 'isoforms')
Default: 'genes'
output_directory : str
Path to location, where csvs should be stored. Default: "" –> current directory is used
return_result : bool
Whether result should be returned. If false nothing is returned. Default: False

Returns

Proteo map text file

def export_sbtab(self, filename='', add_links=False, return_result=False)

Exports simulation data in one single sbtab file

Parameters

filename : str
Name, under which to save SBtab-file
add_links : str
Wheter to implement entry-format, which allows links between table-elements.
return_result : bool
Whether result should be returned. If false nothing is returned. Default: False

Returns

SBtab

def export_xml(self)

Exports xml-file

def from_json(self, inputString)

Imports data from JSON string object Parameters

inputString : json-string
 
def from_simulation_results(self, rbaSession, session_name='')

Imports data from rbatools.RBA_Controler object Parameters

rbaSession : SessionRBA
Defines from which object to extract the data from
session_name : str
Defines the name of the session Is appended to the filenames generated by export methods.