HARMONY scripts

This repository contains a number of example python scripts that make it easier to deal with Combine Archives

Get started

Clone the repository, create a new virtual environment. And install the requirements:

pip install -r requirements.txt

make changes, commit and have fun. Or add issues on what would be nice to have.

Command Line tools

You could also just install the package and use it straight from the command line. Again i'd use a virtual environment for that:

python3 -m venv venv
. ./venv/bin/activate

then install with:

pip install git+git://github.com/fbergmann/harmony_scripts#egg=harmony_scripts

this gives you the following two command line scripts:

• check_omex: just checks the given omex file, to see if all files are in there and if it contains SED-ML files whether those contain all models
• export_copasi_sedml: given a copasi file, this lets you export it as SED-ML, allowing to specify the SBML filename and where to place it.

To test whether the installation works you can run:

(venv) frank@BQFRANK:/tmp#  python -m harmony_scripts
HARMONY utility scripts

    Uses:
        COPASI 4.30.240
        libSBML 5.19.0
        libSEDML 2.0.18
        libCOMBINE 0.2.10

    Provides the command line functions:

        check_omex <omex file> <tempdir>
        export_copasi_sedml <cps file file> <sedml_name> <sbml_name> <output_dir>

Examples check_omex

The check_omex command will check the given omex archive, for the following things:

• sbml models referenced from SED-ML files, do exist in the archive
• the SED-ML / SBML files are valid
• ids are not duplicated in the SED-ML file
• xpath expressions from the SED-ML file do resolve in the SBML file

Called without arg:

(venv) frank@BQFRANK:/tmp# check_omex
usage check_omex <omex file> <tempdir>

Called with arg:

(venv) frank@BQFRANK:/tmp# check_omex ./harmony_scripts/examples/BIOMD0000000791-20210325-094855.omex /tmp
ERROR:root:missing model file model.xml

Testing a biomodel:

(venv) frank@BQFRANK:/tmp#  curl -L http://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000001 -o BIOMD0000000001.omex
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                               	 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  277k    0  277k    0     0   131k      0 --:--:--  0:00:02 --:--:--  160k
(venv) frank@BQFRANK:/tmp#  check_omex ./BIOMD0000000001.omex /tmp
(venv) frank@BQFRANK:/tmp# 

And another test:

(venv) frank@BQFRANK:/tmp#  curl -L http://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000791 -o BIOMD0000000791.omex
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                             	 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 15980    0 15980    0     0  10760      0 --:--:--  0:00:01 --:--:--  200k
(venv) frank@BQFRANK:/tmp# check_omex ./BIOMD0000000791.omex /tmp
ERROR:root:missing model file model.xml in sedml-file Wilson2012	
(venv) frank@BQFRANK:/tmp# 

Examples export_copasi_sedml

Called without arg:

(venv) frank@BQFRANK:/tmp# export_copasi_sedml
usage export_copasi_sedml <cps file file> <sedml_name> <sbml_name> <output_dir>

Called with arg:

(venv) frank@BQFRANK:/tmp# export_copasi_sedml ./harmony_scripts/examples/Wilson2012.cps Wilson2012.sedml Wilson2012.xml /tmp

(venv) frank@BQFRANK:/tmp# ls *Wi*
Wilson2012.sedml  Wilson2012.xml	

(venv) frank@BQFRANK:/tmp# cat Wilson2012.sedml  | grep "<model"
<model id="model" language="urn:sedml:language:sbml" source="Wilson2012.xml"/>

Examples check_sbml

This script validates SBML files

Called without arg:

(venv) frank@BQFRANK:/tmp# check_sbml
usage: check_sbml <sbml file>

Called with arg:

(venv) frank@BQFRANK:/tmp# check_sbml ./harmony_scripts/examples/Wilson2012.xml

Examples inline_function_definitions

This script modifies the SBML file given, to inline all function definitions. If only one argument is given, the source file will be overwritten, otherwise the output file will be created.

Called without arg:

(venv) frank@BQFRANK:/tmp# inline_function_definitions
usage: inline_function_definitions <sbml file> [output file]

Called with arg:

(venv) frank@BQFRANK:/tmp# inline_function_definitions ./harmony_scripts/examples/Wilson2012.xml ./out/Wilson2012.xml

License

Just as COPASI, the packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.