Installation

You can install ingranalyze by running:

$ pip3 install --user ingranalyze

On Linux the executable script can then be found in ~/.local/bin

and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/3.2/bin.

Usage

Typical usage is:

$ ingranalyze.py --mics --repair 5 networkfile observationfile

For more options you can ask for help as follows:

$ ingranalyze.py -h
usage: ingranalyze.py [-h] [--mics] [--repair {1,2,3,4,5}] [--list_repairs] networkfile observationfile
positional arguments:
  networkfile           influence graph in bioquali format
  observationfile       observations in bioquali format

optional arguments:
  -h, --help            show this help message and exit
  --mics                compute minimal inconsistent cores
  --repair {1,2,3,4,5}  choose repair method: 1 flip observed variations, 2
                        flip influences, 3 define network nodes as inputs, 4
                        define network nodes as input in an experiment (use
                        only in case of multiple experiments), 5 add
                        influences. default is 3
  --list_repairs        compute all minimal repair sets

Samples

Sample files for yeast are available here: yeast_guelzim.net and yeast_snf2.obs