booldog.io

Mixins that expose BoolDogModel.from_XXX/to_XXX constructors and exporters, dispatching to the reader/writer functions implemented in the sibling booldog.io modules (one module per supported file/object format).

Submodules

Attributes

logger

Classes

`BoolDogModelIOFromMixin`	Mixin providing BoolDogModel.from_XXX constructors
`BoolDogModelIOToMixin`	Mixin providing to_XXX export methods for supported Boolean / regulatory network formats.

Package Contents

booldog.io.logger

class booldog.io.BoolDogModelIOFromMixin

Mixin providing BoolDogModel.from_XXX constructors for supported Boolean / regulatory network formats.

classmethod _from_reader(reader, *args, **kwargs)

Generic constructor wrapper around a reader function.

Reader functions should take *args and **kwargs as input and return a dictionary of “nodes”, “modelinfo” and “primes” (primes and modelinfo are optional, but “nodes” is required).

classmethod from_bnet(*args, **kwargs)

Create model from BoolNet .bnet format.

Forwards all arguments to booldog.io.bnet.read_bnet().

classmethod from_primes(*args, **kwargs)

Create model from prime implicants format.

Forwards all arguments to booldog.io.primes.read_primes().

classmethod from_sbmlqual(*args, **kwargs)

Create model from SBML-qual file.

Forwards all arguments to booldog.io.sbml.read_sbmlqual().

classmethod from_tabularqual(*args, **kwargs)

Create model from tabular-qual format.

Forwards all arguments to booldog.io.tabularqual.read_tabularqual().

classmethod from_interactions(*args, **kwargs)

Create model from generic interaction table.

Forwards all arguments to booldog.io.interaction_networks.read_interactions().

classmethod from_sif(*args, **kwargs)

Create model from SIF interaction network.

Forwards all arguments to booldog.io.interaction_networks.read_sif().

classmethod from_networkx(*args, **kwargs)

Create model from networkx graph.

Forwards all arguments to booldog.io.interaction_networks.read_networkx().

classmethod from_igraph(*args, **kwargs)

Create model from igraph object or file.

Forwards all arguments to booldog.io.interaction_networks.read_igraph().

classmethod from_graphml(*args, **kwargs)

Create model from GraphML file.

Forwards all arguments to booldog.io.interaction_networks.read_graphml().

class booldog.io.BoolDogModelIOToMixin

Mixin providing to_XXX export methods for supported Boolean / regulatory network formats.

classmethod _to_writer(writer, *args, **kwargs)

Generic constructor wrapper around a writer function.

Writer functions should take *args and **kwargs as input and return a string or write to a file. The first argument should always be the model instance (self). An optional keyword argument “outfile” can be used to specify an output file path.

This constructor presents a consistent interface for exporting models to various formats, and centralizes any common logic needed.