casq-fork

https://github.com/sybila/casq-fork

Repository

README.rst

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

This extension allows also generating partially specified Boolean networks in .aeon
format from `CellDesigner`_ models. Possible use in `AEON`_ tool for further
analyses.

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

Install
=======

CaSQ is provided as a Python3 package, you can install it from the
https://github.com/sybila/casq-fork.git.


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 ...]] [-a] [-b] [-g GRANULARITY] [-i INPUT] [-C]
            [infile] [outfile]

    Convert CellDesigner models to SBML-qual with a rather strict semantics.
    Copyright (C) 2019, Sylvain.Soliman@inria.fr GPLv3.
    Convert CellDesigner models to partially specified Boolean networks in .aeon format.
    Copyright (C) 2024, xfrak@fi.muni.cz GPLv3.

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

    options:
      -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
      -a, --aeon            Output to partially specified Boolean networks in .aeon format
      -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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