io Package

io Package

mat Module

cobra.io.mat.load_matlab_model(infile_path, variable_name=None)[source]

Load a cobra model stored as a .mat file .. warning:: INCOMPLETE, does not load GPR’s

infile_path : str 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
cobra.io.mat.save_matlab_model(model, file_name)[source]

Save the cobra model as a .mat file.

This .mat file can be used directly in the MATLAB version of COBRA. .. note:: This function works best with scipy 0.11b1 or later

model : cobra.Model file_name : str or file-like object

sbml Module

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

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

sbml_model: sbml_model object

cobra_metabolite: a cobra.Metabolite object

note_start_tag: the start tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml.

note_end_tag: the end tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml.

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

convert an SBML XML file into a cobra.Model object. Supports SBML Level 2 Versions 1 and 4

sbml_filename: String.

old_sbml: Boolean. 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: Boolean. 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: Boolean. Print the time requirements for different sections

use_hyphens: Boolean. If True, double underscores (__) in an SBML ID will be converted to hyphens

cobra.io.sbml.fix_legacy_id(id, use_hyphens=False)[source]
cobra.io.sbml.parse_legacy_id(the_id, the_compartment=None, the_type='metabolite', use_hyphens=False)[source]

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

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

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

Deal with legacy SBML format issues arising from the COBRA Toolbox for MATLAB and BiGG.ucsd.edu developers.

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

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)[source]

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

cobra_model: A cobra.Model object

sbml_filename: The file to write the SBML XML to.

sbml_level: 2 is the only level supported at the moment.

sbml_version: 1 is the only version supported at the moment.

print_time: Boolean. Print the time requirements for different sections

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

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