wholecell.utils.toya
Utilities for working with TOYA data
- wholecell.utils.toya.adjust_toya_data(data, cell_masses, dry_masses, cell_density)[source]
Adjust fluxes or stdevs for dry mass fraction, density, units.
The provided data are multiplied by the average dry mass fraction and by the cell density.
- Parameters:
data (ndarray[Any, dtype[float64]]) – Flux or standard deviation data vector to process.
cell_masses (ndarray[Any, dtype[float64]]) – Vector of cell mass over time. Units should be stored elementwise.
dry_masses (ndarray[Any, dtype[float64]]) – Vector of cell dry mass over time. Units should be stored elementwise.
cell_density (float) – Constant density of cell.
- Returns:
Vector of adjusted data. Units are applied to the whole vector.
- Return type:
Unum
- wholecell.utils.toya.get_root_to_id_indices_map(sim_reaction_ids)[source]
Get a map from ID root to indices in sim_reaction_ids
The reaction root is the portion of the ID that precedes the first underscore or space.
- wholecell.utils.toya.process_simulated_fluxes(output_ids, reaction_ids, reaction_fluxes)[source]
Compute means and standard deviations of flux from simulation
For a given output ID from output_ids, find the mean and stdev of simulated fluxes of the reaction with the matching ID.
- Parameters:
output_ids (Iterable[str]) – IDs of reactions to include in output
reaction_ids (Iterable[str]) – IDs of the reactions in the order that they appear in reaction_fluxes
reaction_fluxes (Unum) – 2-dimensional matrix of reaction fluxes where each column corresponds to a reaction (in the order specified by reaction_ids) and each row is a time point. Should have units FLUX_UNITS and be a numpy matrix.
- Returns:
Tuple of the lists of mean fluxes and standard deviations for each reaction ID in output_ids. List elements are in the same order as their associated reaction IDs in output_ids. Both lists will have units FLUX_UNITS.
- Return type:
tuple[Unum, Unum]
- wholecell.utils.toya.process_toya_data(output_ids, reaction_ids, data)[source]
Filter toya fluxes or standard deviations by reaction ID
- Parameters:
output_ids (Iterable[str]) – IDs of reactions to include in the output.
reaction_ids (Iterable[str]) – IDs of the reactions whose fluxes and standard deviations are provided, in the order in which the rections’ values appear in fluxes and stdevs.
data (Unum) – 1-dimensional numpy array (with units FLUX_UNITS) with average reaction fluxes or standard deviations.
- Returns:
List of data in the order specified by output_ids. List is of units FLUX_UNITS.
- Return type:
Unum