cobra.io.web
¶
Provide functionality to access remote model repositories.
Submodules¶
Package Contents¶
Classes¶
Define an abstract base class that describes a remote model repository. |
|
Define a concrete implementation of the BiGG Models repository. |
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Define a concrete implementation of the BioModels repository. |
Functions¶
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Download an SBML model from a remote repository. |
- class cobra.io.web.AbstractModelRepository(*, url: Union[httpx.URL, str], **kwargs)[source]¶
Bases:
abc.ABC
Define an abstract base class that describes a remote model repository.
- property url: httpx.URL¶
Return the repository’s URL.
- _progress¶
- class cobra.io.web.BiGGModels(**kwargs)[source]¶
Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepository
Define a concrete implementation of the BiGG Models repository.
- class cobra.io.web.BioModels(**kwargs)[source]¶
Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepository
Define a concrete implementation of the BioModels repository.
- cobra.io.web.load_model(model_id: str, repositories: Iterable[cobra.io.web.abstract_model_repository.AbstractModelRepository] = DEFAULT_REPOSITORIES, cache: bool = True) cobra.core.Model [source]¶
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
AbstractModelRepository
class as a parent to implement your own repository accessor which you pass to theload_model
function. 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