file_exchange

bnet2primes(bnet: str, fname_primes: Optional[str] = None) → dict

Generates and returns the prime implicants of a Boolean network in boolnet format. The primes are saved as a json file if fname_primes is given. The argument bnet may be either the name of a bnet file or a string containing the file contents. Use the function read_primes to open a previously saved json file.

arguments:

  • bnet: name of bnet file or string contents of file

  • fname_primes: None or name of json file to save primes

returns:

  • primes: prime implicants

example:

>>> primes = bnet2primes("mapk.bnet", "mapk.primes" )
>>> primes = bnet2primes("mapk.bnet")
>>> primes = bnet2primes("Erk, !Mek \n Raf, Ras & Mek")
>>> primes = bnet2primes("Erk, !Mek \n Raf, Ras & Mek", "mapk.primes")
primes2bnet(primes: dict, fname_bnet: Optional[str] = None, minimize: bool = False, header: bool = False) → str

Saves primes as a bnet file, including the header “targets, factors” for compatibility with BoolNet. Without minimization, the resuting formulas are disjunctions of all prime implicants and may therefore be very long. If Minimize=True then a Python version of the Quine-McCluskey algorithm, namely Prekas2012 which is implemented in QuineMcCluskey.primes2mindnf, will be used to minimize the number of clauses for each update function.

arguments:

  • primes: prime implicants

  • fname_bnet: name of bnet file or None for the string of the file contents

  • minimize: minimize the Boolean expressions

  • header: whether to include the “targets, factors” header

returns:

  • text_bnet: str contents of bnet file

example:

>>> primes2bnet(primes, "mapk.bnet")
>>> primes2bnet(primes, "mapk.bnet", True)
>>> expr = primes2bnet(primes)
>>> expr = primes2bnet(primes, True)
primes2bns(primes: dict, fname_bns: Optional[str] = None) → str

Saves Primes as a bns file for the computation of all attractors of the synchronous transition system. BNS_ is based on Dubrova2011. It is available at http://people.kth.se/~dubrova/bns.html.

arguments:

  • primes: prime implicants

  • fname_bns: name of bns file or None to return file as string

example:

>>> primes2bns(primes, "mapk.bns")
primes2eqn(primes: dict, fname_eqn: Optional[str] = None) → str

Generates a eqn file as specified in the manual for the model checking software Antelope_ from primes. Antelope_ was introduced in Arellano2011.

arguments:

  • primes: prime implicants

  • fname_eqn: name of eqn file

example:

>>> primes2eqn(primes, "mapk.eqn")
primes2genysis(primes: dict, fname_genysis: str)

Generates a GenYsis_ file from primes for the computation of all attractors of the synchronous or asynchronous transition system. GenYsis_ was introduced in Garg2008. It is available at http://www.vital-it.ch/software/genYsis.

arguments:

  • primes: prime implicants

  • fname_genysis: name of GenYsis_ file

example:

>>> primes2genysis(primes, "mapk.genysis")
read_primes(fname_json: str) → dict

Reads the prime implicants of a Boolean network that were previously stored as a json file.

arguments:

  • fname_json: name of json file

returns:

  • primes: prime implicants

example:

>>> primes = read_primes("mapk.primes")
write_primes(primes: dict, fname_json: str)

Saves primes as a json file.

arguments:

  • primes: prime implicants

  • fname_json: name of json file

example:

>>> write_primes(primes, "mapk.primes")