casq

CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]

https://github.com/soli/casq

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CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]

README.rst

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   :target: https://pypi.org/project/casq/

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   :alt: Conda-Forge CaSQ version

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**CaSQ** converts `CellDesigner`_ and `SBGN-ML`_ 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
.. _`SBGN-ML`: https://github.com/sbgn/sbgn/wiki/SBGN_ML
.. _`published article`: https://academic.oup.com/bioinformatics/article/36/16/4473/5836892

Install
=======

CaSQ 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:

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

.. code:: bash

   $ python3 -m pip install casq

Command-line usage
==================

Just follow the instructions::

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

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

   positional arguments:
     infile                CellDesigner or SBGN-ML 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 (and
                           .bnet) 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)
     -f FIXED, --fixed FIXED
                           A CSV file containing input values or knock-ins/knock-
                           outs, one per line, with name in the first column and
                           the value in the second.
     -n, --names           Use the names as IDs in the SBML file
     -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
     -i INPUT, --input INPUT
                           When exporting to BMA, nodes with no input should be
                           set to this value
     -C, --colourConstant  When exporting to BMA, colour all variables pink
                           (defaults to colour by compartment)

Owner

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: CaSQ
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Sylvain
    family-names: Soliman
    email: Sylvain.Soliman@inria.fr
    affiliation: Inria
    orcid: 'https://orcid.org/0000-0001-5525-7418'
  - given-names: Anna
    family-names: Niarakis
    email: Anna.Niaraki@univ-evry.fr
    affiliation: 'GenHotel, Université d''Évry'
    orcid: 'https://orcid.org/0000-0002-9687-7426'
repository-code: 'https://gitlab.inria.fr/soliman/casq/'
url: 'https://casq.readthedocs.io/en/stable/'
license: GPL-3.0
preferred-citation:
  type: article
  authors:
  - given-names: Sara
    family-names: Sadat Aghamiri
    affiliation: 'GenHotel, Université d''Évry'
  - given-names: Vidisha
    family-names: Singh
    affiliation: 'GenHotel, Université d''Évry'
  - given-names: Aurélien
    family-names: Naldi
    affiliation: 'Institut de Biologie de l''École Normale Supérieure'
  - given-names: Tomáš
    family-names: Helikar
    affiliation: 'Department of Biochemistry, University of Nebraska-Lincoln'
  - given-names: Sylvain
    family-names: Soliman
    email: Sylvain.Soliman@inria.fr
    affiliation: Inria
    orcid: 'https://orcid.org/0000-0001-5525-7418'
  - given-names: Anna
    family-names: Niarakis
    email: Anna.Niaraki@univ-evry.fr
    affiliation: 'GenHotel, Université d''Évry'
    orcid: 'https://orcid.org/0000-0002-9687-7426'
  doi: "10.1093/bioinformatics/btaa484"
  journal: "Bioinformatics"
  month: 5
  start: 4473
  end: 4482
  title: "Automated inference of Boolean models from molecular interaction maps using CaSQ"
  issue: 16
  volume: 36
  year: 2020

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