booldog.io.bnet
===============

.. py:module:: booldog.io.bnet

.. autoapi-nested-parse::

   Additional functions to parse bnet format



Attributes
----------

.. autoapisummary::

   booldog.io.bnet.logger
   booldog.io.bnet.BNET_LINE_REGEX
   booldog.io.bnet.BNET_REGULATORS_REGEX
   booldog.io.bnet.BNET_HEADER


Classes
-------

.. autoapisummary::

   booldog.io.bnet.BnetParser


Functions
---------

.. autoapisummary::

   booldog.io.bnet.read_bnet
   booldog.io.bnet.write_bnet


Module Contents
---------------

.. py:data:: logger

.. py:data:: BNET_LINE_REGEX
   :value: '^[a-zA-Z]+[a-zA-Z0-9_]*,\\s*.+$'


.. py:data:: BNET_REGULATORS_REGEX
   :value: '\\b[A-Za-z_][A-Za-z0-9_]*\\b'


.. py:data:: BNET_HEADER
   :value: 'targets, factors'


.. py:class:: BnetParser(bnet)

   .. py:attribute:: bnet


   .. py:attribute:: rules


   .. py:method:: _get_rules(bnet_str)

      Boolean rules per node.





.. py:function:: read_bnet(bnet, node_names=None)

   Generate a BoolDogModel object from a Boolean network in boolnet
   (bnet) format.

   For complete documentation, see :doc:`pyboolnet:modules/file_exchange`.

   :param file: Path to the bnet file
   :type file: str

   :returns: **rn** -- An object of type :ref:`py:class:BoolDogModel`.
   :rtype: BoolDog

   .. rubric:: Notes

   The format of the output file is described at :ref:`boolnet_format`.


.. py:function:: write_bnet(model, outfile=None, from_primes=False, header=True, minimize=False)

   Write a BoolDogModel object to a Boolean network in boolnet (bnet) format.

   :param model: A BoolDog object representing a Boolean network.
   :type model: BoolDogModel
   :param outfile: Path to the output file. If None, the output is returned as a string.
   :type outfile: str
   :param from_primes: If True, rules are obtained by converting prime implicants to bnet
                       format. Otherwise, node rules are written directly.
   :type from_primes: bool, default False
   :param header: If True, include a header line ("target, factors").
   :type header: bool, default True
   :param minimize: If True, minimize rules when converting from primes. Only relevant if
                    ``from_primes`` is True.
   :type minimize: bool, default False

   :returns: Returns the bnet string if ``outfile`` is None, otherwise None.
   :rtype: str or None

   .. rubric:: Notes

   The output file will be overwritten if it already exists.

   The format of the output file is described at :ref:`boolnet_format`.