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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 casqNote 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 v1.4.3Command-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)
2 maintainers
Release files for casq 1.4.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| casq-1.4.4.tar.gz | 620.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| casq-1.4.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 662.1 kB
Release files / casq-1.4.4.tar.gz
| Download URL | casq-1.4.4.tar.gz |
|---|---|
| Size | 620.7 kB |
| Tags | Source |
|
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Release files / casq-1.4.4-py3-none-any.whl
| Download URL | casq-1.4.4-py3-none-any.whl |
|---|---|
| Size | 41.4 kB |
| Tags | Python 3 |
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