15.1.1.3.1.5. cobra.io.sbml3

15.1.1.3.1.5.1. Module Contents

class cobra.io.sbml3.Basic

cobra.io.sbml3.ns(query)

replace prefixes with namespace

cobra.io.sbml3.extract_rdf_annotation(sbml_element, metaid)

class cobra.io.sbml3.CobraSBMLError

cobra.io.sbml3.get_attrib(tag, attribute, type=None, require=False)

cobra.io.sbml3.set_attrib(xml, attribute_name, value)

cobra.io.sbml3.parse_stream(filename)

parses filename or compressed stream to xml

cobra.io.sbml3.clip(string, prefix)

clips a prefix from the beginning of a string if it exists

>>> clip("R_pgi", "R_")
"pgi"

cobra.io.sbml3.strnum(number)

Utility function to convert a number to a string

cobra.io.sbml3.construct_gpr_xml(parent, expression)

create gpr xml under parent node

cobra.io.sbml3.annotate_cobra_from_sbml(cobra_element, sbml_element)

cobra.io.sbml3.annotate_sbml_from_cobra(sbml_element, cobra_element)

cobra.io.sbml3.parse_xml_into_model(xml, number=float)

cobra.io.sbml3.model_to_xml(cobra_model, units=True)

cobra.io.sbml3.read_sbml_model(filename, number=float, **kwargs)

cobra.io.sbml3.validate_sbml_model(filename, check_model=True)

Returns the model along with a list of errors.

Parameters:

• filename (str) – The filename of the SBML model to be validated.
• check_model (bool, optional) – Whether to also check some basic model properties such as reaction boundaries and compartment formulas.

Returns:

• model (Model object) – The cobra model if the file could be read succesfully or None otherwise.
• errors (dict) – Warnings and errors grouped by their respective types.

Raises:

CobraSBMLError – If the file is not a valid SBML Level 3 file with FBC.

cobra.io.sbml3.write_sbml_model(cobra_model, filename, use_fbc_package=True, **kwargs)

cobra.io.sbml3.indent_xml(elem, level=0)

indent xml for pretty printing