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Design experiments to differentiate interaction graph models.

Project description

Installation

You can install exdesi by running:

$ pip install --user exdesi

On Linux the executable scripts can then be found in ~/.local/bin and on MacOS the scripts are under /Users/YOURUSERNAME/Library/Python/3.2/bin.

Usage

Typical usage is:

$ exdesi.py candidate_directory experimental_variables_file

For more options you can ask for help as follows:

$ exdesi.py -h
usage: exdesi.py [-h] [--best_set BEST_SET] [-x EXCLUDE] networkfiles experivarfile

positional arguments:
  networkfiles          directory of influence graphs in SIF format
  experivarfile         experimental variables

optional arguments:
  -h, --help            show this help message and exit
  --best_set BEST_SET   compute best set of experiments maximal number of
                        experiments, default is OFF, 0=unlimited
  -x EXCLUDE, --exclude EXCLUDE
                        exclude experiments described in file EXCLUDE

Example

Sample files available in the data directory. A sample call would be:

$ exdesi.py in_silico_HEK293/candidates_round1/ in_silico_HEK293/expvars.txt -x in_silico_HEK293/exclude1.txt

Project details


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