Using petablint
petablint
is a tool to validate a model against the PEtab standard. When you have installed PEtab, you can simply call it from the command line. It takes the following arguments:
!petablint -h
usage: petablint [-h] [-v] [-s SBML_FILE_NAME] [-o OBSERVABLE_FILE_NAME]
[-m MEASUREMENT_FILE_NAME] [-c CONDITION_FILE_NAME]
[-p PARAMETER_FILE_NAME] [--vis VISUALIZATION_FILE_NAME]
[-y YAML_FILE_NAME]
Check if a set of files adheres to the PEtab format.
optional arguments:
-h, --help show this help message and exit
-v, --verbose More verbose output
-s SBML_FILE_NAME, --sbml SBML_FILE_NAME
SBML model filename
-o OBSERVABLE_FILE_NAME, --observables OBSERVABLE_FILE_NAME
Observable table
-m MEASUREMENT_FILE_NAME, --measurements MEASUREMENT_FILE_NAME
Measurement table
-c CONDITION_FILE_NAME, --conditions CONDITION_FILE_NAME
Conditions table
-p PARAMETER_FILE_NAME, --parameters PARAMETER_FILE_NAME
Parameter table
--vis VISUALIZATION_FILE_NAME, --visualizations VISUALIZATION_FILE_NAME
Visualization table
-y YAML_FILE_NAME, --yaml YAML_FILE_NAME
PEtab YAML problem filename
Let’s look at an example: In the example_Fujita folder, we have a PEtab configuration file Fujita.yaml
telling which files belong to the Fujita model:
!cat example_Fujita/Fujita.yaml
parameter_file: Fujita_parameters.tsv
format_version: 1
problems:
- condition_files:
- Fujita_experimentalCondition.tsv
measurement_files:
- Fujita_measurementData.tsv
sbml_files:
- Fujita_model.xml
observable_files:
- Fujita_observables.tsv
To verify everything is ok, we can just call:
!petablint -y example_Fujita/Fujita.yaml
Visualization table not available. Skipping.
If there were some inconsistency or error, we would see that here. petablint
can be called in different ways. You can e.g. also pass SBML, measurement, condition, and parameter file directly, or, if the files follow PEtab naming conventions, you can just pass the model name.