casq

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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_.

.. _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 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] [-u [UPSTREAM ...]] [-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY] [-i INPUT] [-C] [infile] [outfile]

Convert CellDesigner models to SBML-qual with a rather strict semantics. Copyright (C) 2019, [e-mail] 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 -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)