sbmlutils.manipulation

Package for SBML manipulation.

Functions for SBML model manipulation.

These functions take existing SBML model(s) and provide common manipulations. For example merging of models or promoting of local parameters.

Submodules

Package Contents

Functions

merge_models(model_paths, output_dir[, merged_id, ...])

Merge SBML models.
sbmlutils.manipulation.merge_models(model_paths, output_dir, merged_id='merged', flatten=True, validate=True, validate_input=True, validation_options=None, sbml_level=3, sbml_version=1)[source]

Merge SBML models.

Merges SBML models given in model_paths in the output_dir. Models are provided as dictionary {

‘model1_id’: model1_path, ‘model2_id’: model2_path, …

} The model ids are used as ids for the ExternalModelDefinitions. Relative paths are set in the merged models.

The created model is either in SBML L3V1 (default) or SBML L3V2.

Parameters:

  • model_paths (Dict[str, pathlib.Path]) – absolute paths to models

  • output_dir (pathlib.Path) – output directory for merged model

  • merged_id (str) – model id of the merged model

  • flatten (bool) – flattens the merged model

  • validate (bool) – boolean flag to validate the merged model

  • validate_input (bool) – boolean flag to validate the input models

  • validation_options (Optional[sbmlutils.validation.ValidationOptions]) – ValidationOptions

  • sbml_level (int) – SBML Level of the merged model in [3]

  • sbml_version (int) – SBML Version of the merged model in [1, 2]

Returns:

SBMLDocument of the merged models

Return type:

libsbml.SBMLDocument