casq 1.4.3

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

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)