Metadata-Version: 2.1
Name: casq
Version: 1.1.3
Summary: CaSQ: Celldesigner as Sbml-Qual
Project-URL: Code, https://gitlab.inria.fr/soliman/casq/
Project-URL: Documentation, https://casq.readthedocs.io/en/latest/
Project-URL: Homepage, https://soliman.gitlabpages.inria.fr/casq/
Project-URL: Mirror, https://github.com/soli/casq
Author-email: Sylvain Soliman <Sylvain.Soliman@inria.fr>
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.7
Requires-Dist: loguru>=0.2.5
Requires-Dist: networkx>=2.2
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: flake8-mypy; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx; extra == 'docs'
Description-Content-Type: text/x-rst

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|pipeline status| |coverage report| |black| |rtd| |gpl|

|pypi-version| |pypi-python| |pypi-wheel| |pypi-downloads| |deps|

.. |pipeline status| image:: https://gitlab.inria.fr/soliman/casq/badges/master/pipeline.svg
   :target: https://gitlab.inria.fr/soliman/casq/commits/master
   :alt: pipeline status

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   :target: https://gitlab.inria.fr/soliman/casq/commits/master
   :alt: coverage report

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/python/black
   :alt: Code style: black

.. |rtd| image:: https://readthedocs.org/projects/casq/badge/?version=latest
   :target: https://casq.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

.. |gpl| image:: https://img.shields.io/pypi/l/casq
   :target: https://gitlab.inria.fr/soliman/casq/raw/master/LICENSE
   :alt: PyPI - License

.. |pypi-version| image:: https://img.shields.io/pypi/v/casq
   :target: https://pypi.org/project/casq/
   :alt: PyPI

.. |pypi-python| image:: https://img.shields.io/pypi/pyversions/casq
   :alt: PyPI - Python Version
   :target: https://pypi.org/project/casq/

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   :target: https://pypi.org/project/casq/
   :alt: PyPI - Wheel

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   :alt: PyPI - Downloads

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   :target: https://pypi.org/project/casq/
   :alt: Libraries.io dependency status for latest release

**CaSQ** converts `CellDesigner`_ models to Boolean models encoded in
`SBML-Qual`_ with a rather strict semantics defined in a
`published article`_.

.. _`CellDesigner`: http://celldesigner.org
.. _`SBML-Qual`: http://sbml.org
.. _`published article`: https://academic.oup.com/bioinformatics/article/36/16/4473/5836892

Install
=======

CaSQ is provided as a Python (>= 3.5) package, you can install it from the `Python package index`_ with ``pip``, ``conda`` or your Python package manager of choice:

.. _`Python package index`: https://pypi.org/project/casq/

.. code:: bash

   $ pip3 install casq

Usage
=====

Just follow the instructions::

   $ casq --help
   usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-u [UPSTREAM ...]]
               [-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY] [-C]
               [infile] [outfile]

   Convert CellDesigner models to SBML-qual with a rather strict semantics.
   Copyright (C) 2019-2022 Sylvain.Soliman@inria.fr GPLv3

   positional arguments:
     infile                CellDesigner File
     outfile               SBML-Qual/BMA json File

   optional arguments:
     -h, --help            show this help message and exit
     -v, --version         show program's version number and exit
     -D, --debug           Display a lot of debug information
     -c, --csv             Store the species information in a separate CSV file
     -s, --sif             Store the influence information in a separate SIF file
     -r S, --remove S      Delete connected components in the resulting model if
                           their size is smaller than S. A negative S leads to
                           keep only the biggest(s) connected component(s)
     -u [UPSTREAM ...], --upstream [UPSTREAM ...]
                           Only species upstream of this/these species will be
                           kept
     -d [DOWNSTREAM ...], --downstream [DOWNSTREAM ...]
                           Only species downstream of this/these species will be
                           kept
     -b, --bma             Output to BMA json format
     -g GRANULARITY, --granularity GRANULARITY
                           When exporting to BMA, use this granularity
     -C, --colourConstant  When exporting to BMA, colour all variables pink
                           (defaults to colour by compartment)
