casq 1.4.4

CaSQ: Celldesigner as Sbml-Qual

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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.

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:

$ 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:

$ 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, [e-mail] 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)