17.1.1.3. cobra.io¶
Provide functions for loading and saving metabolic models.
17.1.1.3.1. Subpackages¶
17.1.1.3.2. Submodules¶
17.1.1.3.3. Package Contents¶
17.1.1.3.3.1. Classes¶
Define an abstract base class that describes a remote model repository. |
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Define a concrete implementation of the BiGG Models repository. |
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Define a concrete implementation of the BioModels repository. |
17.1.1.3.3.2. Functions¶
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Build a model from a dict. |
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Convert model to a dict. |
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Load a cobra model from a JSON string. |
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Load a cobra model from a file in JSON format. |
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Write the cobra model to a file in JSON format. |
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Return the model as a JSON string. |
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Load a cobra model stored as a .mat file. |
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Save the cobra model as a .mat file. |
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Reads SBML model from given filename. |
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Writes cobra model to filename. |
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Validate SBML model and returns the model along with a list of errors. |
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Load a cobra model from a YAML document. |
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Load a cobra model from a file in YAML format. |
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Write the cobra model to a file in YAML format. |
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Return the model as a YAML document. |
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Download an SBML model from a remote repository. |
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cobra.io.model_from_dict(obj)[source]¶ Build a model from a dict.
Models stored in json are first formulated as a dict that can be read to cobra model using this function.
- Parameters
obj (dict) – A dictionary with elements, ‘genes’, ‘compartments’, ‘id’, ‘metabolites’, ‘notes’ and ‘reactions’; where ‘metabolites’, ‘genes’ and ‘metabolites’ are in turn lists with dictionaries holding all attributes to form the corresponding object.
- Returns
The generated model.
- Return type
cora.core.Model
See also
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cobra.io.model_to_dict(model, sort=False)[source]¶ Convert model to a dict.
- Parameters
model (cobra.Model) – The model to reformulate as a dict.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model.
- Returns
A dictionary with elements, ‘genes’, ‘compartments’, ‘id’, ‘metabolites’, ‘notes’ and ‘reactions’; where ‘metabolites’, ‘genes’ and ‘metabolites’ are in turn lists with dictionaries holding all attributes to form the corresponding object.
- Return type
OrderedDict
See also
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cobra.io.from_json(document: str) → 'Model'[source]¶ Load a cobra model from a JSON string.
- Parameters
document (str) – The JSON string representation of a cobra model.
- Returns
The cobra model as interpreted from the JSON string.
- Return type
See also
load_json_model()Load directly from a file.
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cobra.io.load_json_model(filename: str) → 'Model'[source]¶ 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
See also
from_json()Load from a JSON string.
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cobra.io.save_json_model(model: Model, filename: str, sort: bool = False, pretty: bool = False, **kwargs: Any) → None[source]¶ Write the cobra model to a file in JSON format.
- 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.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).
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 (default False).
**kwargs (Any) – Keyword arguments passed to json.dump.
See also
to_json()Return a string representation.
json.dump()Base function.
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cobra.io.to_json(model: Model, sort: bool = False, **kwargs: Any) → str[source]¶ Return the model as a JSON string.
- Parameters
model (cobra.Model) – The cobra model to represent.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).
**kwargs (Any) – Keyword arguments passed on to json.dumps.
- Returns
JSON string representation of the cobra model.
- Return type
See also
save_json_model()Write directly to a file.
json.dumps()Base function.
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cobra.io.load_matlab_model(infile_path, variable_name=None, inf=inf)[source]¶ 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
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cobra.io.save_matlab_model(model, file_name, varname=None)[source]¶ 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
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cobra.io.read_sbml_model(filename, number=float, f_replace=F_REPLACE, **kwargs)[source]¶ Reads SBML model from given filename.
If the given filename ends with the suffix ‘’.gz’’ (for example, ‘’myfile.xml.gz’),’ the file is assumed to be compressed in gzip format and will be automatically decompressed upon reading. Similarly, if the given filename ends with ‘’.zip’’ or ‘’.bz2’,’ the file is assumed to be compressed in zip or bzip2 format (respectively). Files whose names lack these suffixes will be read uncompressed. Note that if the file is in zip format but the archive contains more than one file, only the first file in the archive will be read and the rest ignored.
To read a gzip/zip file, libSBML needs to be configured and linked with the zlib library at compile time. It also needs to be linked with the bzip2 library to read files in bzip2 format. (Both of these are the default configurations for libSBML.)
This function supports SBML with FBC-v1 and FBC-v2. FBC-v1 models are converted to FBC-v2 models before reading.
The parser tries to fall back to information in notes dictionaries if information is not available in the FBC packages, e.g., CHARGE, FORMULA on species, or GENE_ASSOCIATION, SUBSYSTEM on reactions.
- Parameters
filename (path to SBML file, or SBML string, or SBML file handle) – SBML which is read into cobra model
number (data type of stoichiometry: {float, int}) – In which data type should the stoichiometry be parsed.
f_replace (dict of replacement functions for id replacement) – Dictionary of replacement functions for gene, specie, and reaction. By default the following id changes are performed on import: clip G_ from genes, clip M_ from species, clip R_ from reactions If no replacements should be performed, set f_replace={}, None
- Returns
- Return type
Notes
- Provided file handles cannot be opened in binary mode, i.e., use
- with open(path, “r” as f):
read_sbml_model(f)
File handles to compressed files are not supported yet.
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cobra.io.write_sbml_model(cobra_model, filename, f_replace=F_REPLACE, **kwargs)[source]¶ Writes cobra model to filename.
The created model is SBML level 3 version 1 (L1V3) with fbc package v2 (fbc-v2).
If the given filename ends with the suffix “.gz” (for example, “myfile.xml.gz”), libSBML assumes the caller wants the file to be written compressed in gzip format. Similarly, if the given filename ends with “.zip” or “.bz2”, libSBML assumes the caller wants the file to be compressed in zip or bzip2 format (respectively). Files whose names lack these suffixes will be written uncompressed. Special considerations for the zip format: If the given filename ends with “.zip”, the file placed in the zip archive will have the suffix “.xml” or “.sbml”. For example, the file in the zip archive will be named “test.xml” if the given filename is “test.xml.zip” or “test.zip”. Similarly, the filename in the archive will be “test.sbml” if the given filename is “test.sbml.zip”.
- Parameters
cobra_model (cobra.core.Model) – Model instance which is written to SBML
filename (string) – path to which the model is written
f_replace (dict of replacement functions for id replacement) –
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cobra.io.validate_sbml_model(filename, check_model=True, internal_consistency=True, check_units_consistency=False, check_modeling_practice=False, **kwargs)[source]¶ Validate SBML model and returns the model along with a list of errors.
- Parameters
filename (str) – The filename (or SBML string) of the SBML model to be validated.
internal_consistency (boolean {True, False}) – Check internal consistency.
check_units_consistency (boolean {True, False}) – Check consistency of units.
check_modeling_practice (boolean {True, False}) – Check modeling practise.
check_model (boolean {True, False}) – Whether to also check some basic model properties such as reaction boundaries and compartment formulas.
- Returns
(model, errors)
model (
Modelobject) – The cobra model if the file could be read successfully or None otherwise.errors (dict) – Warnings and errors grouped by their respective types.
- Raises
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cobra.io.from_yaml(document)[source]¶ Load a cobra model from a YAML document.
- Parameters
document (str) – The YAML document representation of a cobra model.
- Returns
The cobra model as represented in the YAML document.
- Return type
See also
load_yaml_model()Load directly from a file.
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cobra.io.load_yaml_model(filename)[source]¶ Load a cobra model from a file in YAML format.
- Parameters
filename (str or file-like) – File path or descriptor that contains the YAML document describing the cobra model.
- Returns
The cobra model as represented in the YAML document.
- Return type
See also
from_yaml()Load from a string.
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cobra.io.save_yaml_model(model, filename, sort=False, **kwargs)[source]¶ Write the cobra model to a file in YAML format.
kwargsare passed on toyaml.dump.- Parameters
model (cobra.Model) – The cobra model to represent.
filename (str or file-like) – File path or descriptor that the YAML representation should be written to.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model.
See also
to_yaml()Return a string representation.
ruamel.yaml.dump()Base function.
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cobra.io.to_yaml(model, sort=False, **kwargs)[source]¶ Return the model as a YAML document.
kwargsare passed on toyaml.dump.- Parameters
model (cobra.Model) – The cobra model to represent.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model.
- Returns
String representation of the cobra model as a YAML document.
- Return type
See also
save_yaml_model()Write directly to a file.
ruamel.yaml.dump()Base function.
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class
cobra.io.AbstractModelRepository(*, url: Union[httpx.URL, str], **kwargs)¶ Bases:
abc.ABCDefine an abstract base class that describes a remote model repository.
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_progress¶
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name:str = Abstract
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property
url(self) → httpx.URL¶ Return the repository’s URL.
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class
cobra.io.BiGGModels(**kwargs)¶ Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepositoryDefine a concrete implementation of the BiGG Models repository.
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name:str = BiGG Models
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get_sbml(self, model_id: str) → bytes¶ Attempt to download an SBML document from the repository.
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class
cobra.io.BioModels(**kwargs)¶ Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepositoryDefine a concrete implementation of the BioModels repository.
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name:str = BioModels
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get_sbml(self, model_id: str) → bytes¶ Attempt to download an SBML document from the repository.
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cobra.io.load_model(model_id: str, repositories: Iterable[AbstractModelRepository] = (BiGGModels(), BioModels()), cache: bool = True) → 'Model'¶ Download an SBML model from a remote repository.
Downloaded SBML documents are by default stored in a cache on disk such that future access is much faster. By default, models can be loaded from the following repositories:
BiGG Models
BioModels
You can use the
AbstractModelRepositoryclass as a parent to implement your own repository accessor which you pass to theload_modelfunction. In case you implement a new interface, please consider submitting a pull request to COBRApy.- Parameters
model_id (str) – The identifier of the desired metabolic model. This is typically repository specific.
repositories (iterable, optional) – An iterable of repository accessor instances. The model_id is searched in order.
cache (bool, optional) – Whether or not to use the local caching mechanism (default yes).
- Returns
A model instance generated from the SBML document.
- Return type
- Raises
RuntimeError – As with any internet connection, there are multiple errors that can occur.
Examples
# Most of the time calling load_model with an identifier should be enough. >>> print(load_model(“e_coli_core”)) e_coli_core >>> print(load_model(“MODEL1510010000”)) MODEL1510010000
See also