booldog.io.sbml

Read-write SBML-qual files

Notes

SBML-qual code is inspired by:

Attributes

_SBML_AVAILABLE

logger

SBML_INT_MAX

TOKEN_REGEX

Exceptions

BoolDogSBMLException

Custom Exception for SBML parsing

Classes

SBMLQualReader

TransitionParser

Parse SBML transition to bnet format

MathMLParser

Parse MathML to bnet format

SBMLQualWriter

Functions

read_sbmlqual(file)

Create Network from a SBML-qual file

write_sbmlqual(model, outfile, **kwargs)

Module Contents

booldog.io.sbml._SBML_AVAILABLE = True
booldog.io.sbml.logger
booldog.io.sbml.SBML_INT_MAX = 2147483647
booldog.io.sbml.TOKEN_REGEX
exception booldog.io.sbml.BoolDogSBMLException

Bases: Exception

Custom Exception for SBML parsing

class booldog.io.sbml.SBMLQualReader(file)
file
document
model
model_id
plugin
all_species
species_names
transitions
rules
_get_qual_plugin()
_get_all_species()
_get_all_transitions()
_get_all_rules()
to_bnet()

Converts the SBML-qual file to a bnet format.

Returns:

bnet – bnet representation of the Boolean network.

Return type:

str

class booldog.io.sbml.TransitionParser

Parse SBML transition to bnet format

static parse_io(transition, all_species)

Extract transition inputs and outputs.

Parameters:

  • transition (libsbml::Transition) – Transition specifying the logical rule associated with the Transition outputs.

  • all_species (list) – List ids of all species present in model

Returns:

  • inputs (dict) – Dictionary of id: species information for this transition’s inputs

  • outputs (list) – List of this transition’s outputs (dependents)

static parse_function(transition, all_species, inputs)

Parse transition function to a logical rule.

Parameters:

  • transition (libsbml::Transition) – Transition specifying the logical rule associated with the Transition outputs.

  • all_species (list) – List ids of all species present in model

  • inputs (dict) – Dictionary of id: species information for this transition’s inputs

Returns:

logic_rule – Logic rule of this transition (in bnet format)

Return type:

str

class booldog.io.sbml.MathMLParser

Parse MathML to bnet format

static parse(node, all_species, inputs, level=0)
static _handle_operator(operator, children, level)
static _handle_xor(children)

Create disjunctive normal form (DNF) of an xor

static _handle_comparison(operator, children)

Return bnet form of an (mathml) operator between two children.

class booldog.io.sbml.SBMLQualWriter(network, level=3, version=1, qual_version=1)
network
mplugin
node_dict
doc
write(outfile)
_add_species()
_add_transitions()
_rule_to_formula(rule, input_node_dict)

Rule (as in bnet) to a formula as supported by parseL3Formula

Notes

Replaces:

  • & with &&

  • | with ||

To support thresholds, we need to replace the bnet format with a format supported by libsbml’s parseL3Formula:

  • A to (A >= theta_A) f”({node_dict[node]} >= {input_node_dict[node]})”

  • !A to (A < theta_A) f”({node_dict[node]} < {input_node_dict[node]})”

This is currently NOT implemented.

booldog.io.sbml.read_sbmlqual(file)

Create Network from a SBML-qual file

Parameters:

file (str) – Path to SBML-qual file.

Notes

The SBML-qual file is converted to a Boolean network using libsbml, via the bnet format. To access the bnet format directly, you can use py:booldog.io.sbmlqual2bnet.

booldog.io.sbml.write_sbmlqual(model, outfile, **kwargs)