15.1.1.3.1.4. cobra.io.sbml

15.1.1.3.1.4.1. Module Contents

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

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.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. 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.parse_legacy_sbml_notes(note_string, note_delimiter=":")[source]

Deal with various legacy SBML format issues.

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)[source]

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

Parameters:

Notes

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

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

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

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.

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

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