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sbml-diff (project homepage)

sbml-diff is a tool for visually representing a single SBML model, or for visually comparing 2 or more SBML models. It can be used in three ways:

  • As a command-line tool (sbml-diff.py)
  • As a python package (see package_demo.py for an example)
  • through our web interface

It relies on elements having id attributes, so does not work with SBML Level 1, but supports files in Level 2 Version 1 - Level 3 Version 1 Core.

Installation

sbml-diff is written in Python 2 (in the future, it is planned to also become compatible with Python 3), and depends on the Beautiful Soup library (installation instructions), with the lxml parser.

Download or git clone the code, cd into the directory, and install using python setup.py install.

This will install both the package and command-line tool.

Commandline usage

usage: sbml-diff.py [-h] [--params] [--kinetics] [--abstract]
                    [--ignore IGNORE] [--elide ELIDE] [--colors COLORS]
                    [--labels LABELS] [--stoich] [--outfile OUTFILE]
                    [--model MODEL] [--align] [--cartoon] [--force]
                    [--hide-params] [--hide-rules] [--complete]
                    infile [infile ...]    

    Summarise one, or compare two or more, SBML models as a network or table.
    Supports five distinct kinds of output:    

    * DOT representation of reaction network (circles representing species, squares representing reactions)
    * DOT representation of an abstraction of reaction network, showing only species (--abstract)
    * DOT representation of a cartoon view of a genetic regulatory network (--cartoon)
    * a table of parameters (--params)
    * a table of kinetic laws for each reaction (--kineticstable)    

    If one or more kinds of table are requested, DOT output is not produced.    


positional arguments:
  infile                List of input SBML files    

optional arguments:
  -h, --help            show this help message and exit
  --params, -p          Print textual comparison of params
  --kinetics, -k        Print textual comparison of kineticLaws
  --abstract, -a        Rather than comparing all reactions, compare abstract
                        regulatory network
  --ignore IGNORE, -i IGNORE
                        List of species to ignore (comma-separated). Works
                        with -a only
  --elide ELIDE, -e ELIDE
                        List of species to elide (comma-separated). Works with
                        -a only
  --colors COLORS, -c COLORS
                        List of colors (comma-separated)
  --labels LABELS, -l LABELS
                        Style for reaction labels (none, name, name+rate,
                        rate)
  --stoich, -s          Also label edges with stoichiometry
  --outfile OUTFILE     Output file
  --model MODEL         Make visual elements not corresponding to the n'th
                        model invisible
  --align               Treat species/reactions with different ids in
                        different models as the same if they have the same set
                        of MIRIAM annnotations
  --cartoon             Draw transcription using SBOL glyphs
  --force, -f           Draw comparison even if files are identical
  --hide-params         Hide parameters modified by rules/events
  --hide-rules          Do not show rules
  --complete            If no changes, exit quietly. Otherwise return param
                        table, kinetic table, and DOT output