sbmlutils.manipulation.merge
¶
Merging of SBML models.
The following is a helper function for merging multiple SBML models into a single model.
Module Contents¶
Functions¶
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Merge SBML models. |
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Create a comp model from given model paths. |
Attributes¶
- sbmlutils.manipulation.merge.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
- sbmlutils.manipulation.merge._create_merged_doc(model_paths, merged_id='merged', sbml_level=3, sbml_version=1)[source]¶
Create a comp model from given model paths.
Warning: This only works if all models are in the same directory.
- Parameters
model_paths (Dict[str, pathlib.Path]) –
merged_id (str) –
sbml_level (int) –
sbml_version (int) –
- Return type
libsbml.SBMLDocument