https://github.com/soli/casq
CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]
https://github.com/soli/casq
sbml
Last synced: about 1 month ago
JSON representation
CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]
- Host: GitHub
- URL: https://github.com/soli/casq
- Owner: soli
- License: gpl-3.0
- Created: 2019-10-15T12:21:43.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2026-01-30T14:34:57.000Z (about 1 month ago)
- Last Synced: 2026-01-31T07:37:41.143Z (about 1 month ago)
- Topics: sbml
- Language: Python
- Homepage: https://casq.readthedocs.io/
- Size: 1.01 MB
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
- Citation: CITATION.cff
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README
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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
Note 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:
.. _`uv`: https://docs.astral.sh/uv/
.. code:: bash
$ uvx casq -v
casq v1.4.3
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 Additionally store the information in a .bnet and
separate CSV files compatible with the Spreadsheet-
SBML-qual format
-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)