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|deps|\n\n|conda| |conda-down| |made-by-humans|\n\n.. |pipeline status| image:: https://gitlab.inria.fr/soliman/casq/badges/master/pipeline.svg\n   :target: https://gitlab.inria.fr/soliman/casq/commits/master\n   :alt: pipeline status\n\n.. |coverage report| image:: https://gitlab.inria.fr/soliman/casq/badges/master/coverage.svg\n   :target: https://gitlab.inria.fr/soliman/casq/commits/master\n   :alt: coverage report\n\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/python/black\n   :alt: Code style: black\n\n.. |rtd| image:: https://readthedocs.org/projects/casq/badge/?version=latest\n   :target: https://casq.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n.. |gpl| image:: https://img.shields.io/pypi/l/casq\n   :target: https://gitlab.inria.fr/soliman/casq/raw/master/LICENSE\n   :alt: PyPI - License\n\n.. |pypi-version| image:: https://img.shields.io/pypi/v/casq\n   :target: https://pypi.org/project/casq/\n   :alt: PyPI\n\n.. |pypi-python| image:: https://img.shields.io/pypi/pyversions/casq\n   :alt: PyPI - Python Version\n   :target: https://pypi.org/project/casq/\n\n.. |pypi-wheel| image:: https://img.shields.io/pypi/wheel/casq\n   :target: https://pypi.org/project/casq/\n   :alt: PyPI - Wheel\n\n.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/casq\n   :target: https://pypi.org/project/casq/\n   :alt: PyPI - Downloads\n\n.. |deps| image:: https://img.shields.io/librariesio/release/pypi/casq\n   :target: https://pypi.org/project/casq/\n   :alt: Libraries.io dependency status for latest release\n\n.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/casq\n   :target: https://anaconda.org/conda-forge/casq\n   :alt: Conda-Forge CaSQ version\n\n.. |conda-down| image:: https://img.shields.io/conda/d/conda-forge/casq\n   :target: https://anaconda.org/conda-forge/casq\n   :alt: Conda-Forge CaSQ total downloads badge\n\n.. |made-by-humans| image:: https://img.shields.io/badge/Made_by-humans-darkviolet\n   :alt: Made by humans\n\n**CaSQ** converts `CellDesigner`_ and `SBGN-ML`_ models to Boolean models\nencoded in `SBML-Qual`_ with a rather strict semantics defined in a `published\narticle`_.\n\n.. _`CellDesigner`: http://celldesigner.org\n.. _`SBML-Qual`: http://sbml.org\n.. _`SBGN-ML`: https://github.com/sbgn/sbgn/wiki/SBGN_ML\n.. _`published article`: https://academic.oup.com/bioinformatics/article/36/16/4473/5836892\n\nInstall\n=======\n\nCaSQ is provided as a Python3 package, you can install it from the `Python package index`_ with ``pip``, ``conda`` or your Python package manager of choice:\n\n.. _`Python package index`: https://pypi.org/project/casq/\n\n.. code:: bash\n\n   $ python3 -m pip install casq\n\nNote that we currently recommend that you use the excellent `uv` tool from Astral, which allows you to run CaSQ without worrying about any installation procedure at all:\n\n.. _`uv`: https://docs.astral.sh/uv/\n\n.. code:: bash\n\n   $ uvx casq -v\n   casq v1.4.3\n\nCommand-line usage\n==================\n\nJust follow the instructions::\n\n   $ casq --help\n   usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-f FIXED] [-n]\n               [-u [UPSTREAM ...]] [-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY]\n               [-i INPUT] [-C]\n               [infile] [outfile]\n\n   Convert CellDesigner/SBGNML models to SBML-qual with a rather strict\n   semantics. 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A negative S leads to\n                           keep only the biggest(s) connected component(s)\n     -f FIXED, --fixed FIXED\n                           A CSV file containing input values or knock-ins/knock-\n                           outs, one per line, with name in the first column and\n                           the value in the second.\n     -n, --names           Use the names as IDs in the SBML file\n     -u [UPSTREAM ...], --upstream [UPSTREAM ...]\n                           Only species upstream of this/these species will be\n                           kept\n     -d [DOWNSTREAM ...], --downstream [DOWNSTREAM ...]\n                           Only species downstream of this/these species will be\n                           kept\n     -b, --bma             Output to BMA json format\n     -g GRANULARITY, --granularity GRANULARITY\n                           When exporting to BMA, use this granularity\n     -i INPUT, --input INPUT\n                           When exporting to BMA, nodes with no input should be\n                           set to this value\n     -C, --colourConstant  When exporting to BMA, colour all variables pink\n                           (defaults to colour by compartment)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoli%2Fcasq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsoli%2Fcasq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoli%2Fcasq/lists"}