SBML merge¶

sbmlutils provides functionality for merging multiple SBML models. The merging uses the SBML comp extension.

In the following example we will merge the first biomodels in a single model. Models are provided as dictionary

{
    'model1_id': model1_path,
    'model2_id': model2_path,
    ...
}

The model_ids are used as ids for the ExternalModelDefinitions and will be the respective prefixes in the flattened model.

[1]:

from pathlib import Path
import tempfile

from sbmlutils.manipulation import merge_models
from sbmlutils import RESOURCES_DIR
from sbmlutils.validation import ValidationOptions


def merge_models_example() -> None:
    """Demonstrate merging of models."""

    input_dir = RESOURCES_DIR / "testdata" / "manipulation" / "merge"

    # dictionary of ids & paths of models which should be combined
    # here we just bring together the first Biomodels
    model_ids = [f"BIOMD000000000{k}" for k in range(1, 5)]
    model_paths = dict(zip(model_ids, [input_dir / f"{mid}.xml" for mid in model_ids]))

    temp_dir = tempfile.TemporaryDirectory()
    merge_models(model_paths, output_dir=temp_dir.name, validation_options=ValidationOptions(units_consistency=False))


if __name__ == "__main__":
    merge_models_example()

WARNING  'output_dir' should be a Path but: '<class 'str'>'                                             merge.py:59

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///home/mkoenig/git/sbmlutils/src/sbmlutils/resources/testdata/manipulation/merge/BIOMD0000000001.xml
valid                    : TRUE
check time (s)           : 0.010

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///home/mkoenig/git/sbmlutils/src/sbmlutils/resources/testdata/manipulation/merge/BIOMD0000000002.xml
valid                    : TRUE
check time (s)           : 0.009

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///home/mkoenig/git/sbmlutils/src/sbmlutils/resources/testdata/manipulation/merge/BIOMD0000000003.xml
valid                    : TRUE
check time (s)           : 0.004

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///home/mkoenig/git/sbmlutils/src/sbmlutils/resources/testdata/manipulation/merge/BIOMD0000000004.xml
valid                    : TRUE
check time (s)           : 0.004

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///tmp/tmphrb1emar/merged.xml
valid                    : TRUE
check time (s)           : 0.054

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

────────────────────────────────────────────────── Flatten SBML ───────────────────────────────────────────────────

<SBMLDocument>
flattend                 : TRUE
flatten time (ms)        : 0.104

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

INFO     Flattened model created: '/tmp/tmphrb1emar/merged_flat.xml'                                 flatten.py:109

────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────

file:///tmp/tmphrb1emar/merged_flat.xml
valid                    : TRUE
check time (s)           : 0.024

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

For the additional options see the API documentation

[2]:

from rich import inspect
inspect(merge_models)

╭─────────────────────────────────── <function merge_models at 0x7feeb82f5b80> ───────────────────────────────────╮
│ def merge_models(model_paths: Dict[str, pathlib.Path], output_dir: pathlib.Path, merged_id: str = 'merged',     │
│ flatten: bool = True, validate: bool = True, validate_input: bool = True, validation_options:                   │
│ Optional[sbmlutils.validation.ValidationOptions] = None, sbml_level: int = 3, sbml_version: int = 1) ->         │
│ libsbml.SBMLDocument:                                                                                           │
│                                                                                                                 │
│ Merge SBML models.                                                                                              │
│                                                                                                                 │
│ 35 attribute(s) not shown. Run inspect(inspect) for options.                                                    │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

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