sbmlutils.io

Helper functions for input/output (IO).

Submodules

Package Contents

Functions

read_sbml(source[, promote, validate, validation_options])

Read SBMLDocument from given source.

validate_sbml(source[, validation_options, title])

Check given SBML source.

write_sbml(doc[, filepath, validate, ...])

Write SBMLDocument to file or string.
sbmlutils.io.read_sbml(source, promote=False, validate=False, validation_options=None)[source]

Read SBMLDocument from given source.

Local parameters can be promoted using the promote flag. Allows to validate the file during reading via the `validate flag. The subset of tested features in validation can be set via the validation_options.

Parameters:

  • source (Union[pathlib.Path, str]) – SBML path or string

  • promote (bool) – promote local parameters to global parameters

  • validate (bool) – validate file

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

Returns:

libsbml.SBMLDocument

Return type:

libsbml.SBMLDocument

sbmlutils.io.validate_sbml(source, validation_options=None, title=None)[source]

Check given SBML source.

Parameters:

  • source (Union[str, pathlib.Path]) – SBML path or string

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

  • title (Optional[str]) – title for validation report (should be filname or model name)

Returns:

ValidationResult

Return type:

sbmlutils.validation.ValidationResult

sbmlutils.io.write_sbml(doc, filepath=None, validate=False, validation_options=None, program_name=None, program_version=None)[source]

Write SBMLDocument to file or string.

To write the SBML to string use ‘filepath=None’, which returns the SBML string.

The file can be validated during writing via the validate flag.

Parameters:

  • doc (libsbml.SBMLDocument) – SBMLDocument to write

  • filepath (Optional[pathlib.Path]) – output file to write

  • validate (bool) – flag for validation

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

  • program_name (Optional[str]) – Program name for SBML file

  • program_version (Optional[str]) – Program version for SBML file

Returns:

None or SBML string

Return type:

Optional[str]