14.1.4. cobra.io package

14.1.4.1. Submodules

14.1.4.2. cobra.io.json module

cobra.io.json.from_json(document)

Load a cobra model from a JSON document.

Parameters:document (str) – The JSON document representation of a cobra model. Returns:The cobra model as represented in the JSON document. Return type:cobra.Model

See also

load_json_model()

Load directly from a file.

cobra.io.json.load_json_model(filename)

Load a cobra model from a file in JSON format.

Parameters:filename (str or file-like) – File path or descriptor that contains the JSON document describing the cobra model. Returns:The cobra model as represented in the JSON document. Return type:cobra.Model

See also

from_json()

Load from a string.

cobra.io.json.save_json_model(model, filename, pretty=False, **kwargs)

Write the cobra model to a file in JSON format.

kwargs are passed on to json.dump.

Parameters:

• model (cobra.Model) – The cobra model to represent.
• filename (str or file-like) – File path or descriptor that the JSON representation should be written to.
• pretty (bool, optional) – Whether to format the JSON more compactly (default) or in a more verbose but easier to read fashion. Can be partially overwritten by the kwargs.

See also

to_json()

Return a string representation.

json.dump()

Base function.

cobra.io.json.to_json(model, **kwargs)

Return the model as a JSON document.

kwargs are passed on to json.dumps.

Parameters:model (cobra.Model) – The cobra model to represent. Returns:String representation of the cobra model as a JSON document. Return type:str

See also

save_json_model()

Write directly to a file.

json.dumps()

Base function.

14.1.4.3. cobra.io.mat module

cobra.io.mat.create_mat_dict(model)

create a dict mapping model attributes to arrays

cobra.io.mat.create_mat_metabolite_id(model)

cobra.io.mat.from_mat_struct(mat_struct, model_id=None, inf=<Mock object>)

create a model from the COBRA toolbox struct

The struct will be a dict read in by scipy.io.loadmat

cobra.io.mat.load_matlab_model(infile_path, variable_name=None, inf=<Mock object>)

Load a cobra model stored as a .mat file

Parameters:

• infile_path (str) – path to the file to to read
• variable_name (str, optional) – The variable name of the model in the .mat file. If this is not specified, then the first MATLAB variable which looks like a COBRA model will be used
• inf (value) – The value to use for infinite bounds. Some solvers do not handle infinite values so for using those, set this to a high numeric value.

Returns:

The resulting cobra model

Return type:

cobra.core.Model.Model

cobra.io.mat.model_to_pymatbridge(model, variable_name='model', matlab=None)

send the model to a MATLAB workspace through pymatbridge

This model can then be manipulated through the COBRA toolbox

Parameters:

• variable_name (str) – The variable name to which the model will be assigned in the MATLAB workspace
• matlab (None or pymatbridge.Matlab instance) – The MATLAB workspace to which the variable will be sent. If this is None, then this will be sent to the same environment used in IPython magics.

cobra.io.mat.save_matlab_model(model, file_name, varname=None)

Save the cobra model as a .mat file.

This .mat file can be used directly in the MATLAB version of COBRA.

Parameters:

• model (cobra.core.Model.Model object) – The model to save
• file_name (str or file-like object) – The file to save to
• varname (string) – The name of the variable within the workspace

14.1.4.4. cobra.io.sbml module

cobra.io.sbml.add_sbml_species(sbml_model, cobra_metabolite, note_start_tag, note_end_tag, boundary_metabolite=False)

A helper function for adding cobra metabolites to an sbml model.

Parameters:

• sbml_model (sbml_model object) –
• cobra_metabolite (a cobra.Metabolite object) –
• note_start_tag (string) – the start tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml.
• note_end_tag (string) – the end tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml.
• boundary_metabolite (bool) – if metabolite boundary condition should be set or not

Returns:

string

Return type:

the created metabolite identifier

cobra.io.sbml.create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False, legacy_metabolite=False, print_time=False, use_hyphens=False)

convert an SBML XML file into a cobra.Model object.

Supports SBML Level 2 Versions 1 and 4. The function will detect if the SBML fbc package is used in the file and run the converter if the fbc package is used.

Parameters:

• sbml_filename (string) –
• old_sbml (bool) – Set to True if the XML file has metabolite formula appended to metabolite names. This was a poorly designed artifact that persists in some models.
• legacy_metabolite (bool) –

  If True then assume that the metabolite id has the compartment id

  appended after an underscore (e.g. _c for cytosol). This has not been implemented but will be soon.

• print_time (bool) – deprecated
• use_hyphens (bool) – If True, double underscores (__) in an SBML ID will be converted to hyphens

Returns:

Model

Return type:

The parsed cobra model

cobra.io.sbml.fix_legacy_id(id, use_hyphens=False, fix_compartments=False)

cobra.io.sbml.get_libsbml_document(cobra_model, sbml_level=2, sbml_version=1, print_time=False, use_fbc_package=True)

Return a libsbml document object for writing to a file. This function is used by write_cobra_model_to_sbml_file().

cobra.io.sbml.parse_legacy_id(the_id, the_compartment=None, the_type='metabolite', use_hyphens=False)

Deals with a bunch of problems due to bigg.ucsd.edu not following SBML standards

Parameters:

• the_id (String.) –
• the_compartment (String) –
• the_type (String) – Currently only ‘metabolite’ is supported
• use_hyphens (Boolean) – If True, double underscores (__) in an SBML ID will be converted to hyphens

Returns:

string

Return type:

the identifier

cobra.io.sbml.parse_legacy_sbml_notes(note_string, note_delimiter=':')

Deal with various legacy SBML format issues.

cobra.io.sbml.read_legacy_sbml(filename, use_hyphens=False)

read in an sbml file and fix the sbml id’s

cobra.io.sbml.write_cobra_model_to_sbml_file(cobra_model, sbml_filename, sbml_level=2, sbml_version=1, print_time=False, use_fbc_package=True)

Write a cobra.Model object to an SBML XML file.

Parameters:

• cobra_model (cobra.core.Model.Model) – The model object to write
• sbml_filename (string) – The file to write the SBML XML to.
• sbml_level (int) – 2 is the only supported level.
• sbml_version (int) – 1 is the only supported version.
• print_time (bool) – deprecated
• use_fbc_package (bool) – Convert the model to the FBC package format to improve portability. http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)

Notes

TODO: Update the NOTES to match the SBML standard and provide support for Level 2 Version 4

14.1.4.5. cobra.io.sbml3 module

exception cobra.io.sbml3.CobraSBMLError

Bases: Exception

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.clip(string, prefix)

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

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

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

create gpr xml under parent node

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

cobra.io.sbml3.get_attrib(tag, attribute, type=<function <lambda>>, require=False)

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

indent xml for pretty printing

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

cobra.io.sbml3.ns(query)

replace prefixes with namespace

cobra.io.sbml3.parse_stream(filename)

parses filename or compressed stream to xml

cobra.io.sbml3.parse_xml_into_model(xml, number=<class 'float'>)

cobra.io.sbml3.read_sbml_model(filename, number=<class 'float'>, **kwargs)

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

cobra.io.sbml3.strnum(number)

Utility function to convert a number to a string

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)

14.1.4.6. Module contents