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:
[1]:
!petablint -h
usage: petablint [-h] [-v] [-s SBML_FILE_NAME] [-m MEASUREMENT_FILE_NAME]
[-c CONDITION_FILE_NAME] [-p PARAMETER_FILE_NAME]
[-y YAML_FILE_NAME | -n MODEL_NAME] [-d DIRECTORY]
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
-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
-y YAML_FILE_NAME, --yaml YAML_FILE_NAME
PEtab YAML problem filename
-n MODEL_NAME, --model-name MODEL_NAME
Model name where all files are in the working
directory and follow PEtab naming convention.
Specifying -[smcp] will override defaults
-d DIRECTORY, --directory DIRECTORY
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:
[2]:
!cat example_Fujita/Fujita.yaml
parameter_file: Fujita_parameters.tsv
petab_version: 0.0.0a17
problems:
- condition_files:
- Fujita_experimentalCondition.tsv
measurement_files:
- Fujita_measurementData.tsv
sbml_files:
- Fujita_model.xml
To verify everything is ok, we can just call:
[3]:
!petablint -y example_Fujita/Fujita.yaml
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.