17.1.1.3.1.1. cobra.io.web
¶
Provide functionality to access remote model repositories.
17.1.1.3.1.1.1. Submodules¶
17.1.1.3.1.1.2. Package Contents¶
17.1.1.3.1.1.2.1. 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. |
17.1.1.3.1.1.2.2. Functions¶
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Download an SBML model from a remote repository. |
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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.
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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.web.
BiGGModels
(**kwargs)[source]¶ Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepository
Define 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.web.
BioModels
(**kwargs)[source]¶ Bases:
cobra.io.web.abstract_model_repository.AbstractModelRepository
Define 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.web.
load_model
(model_id: str, repositories: Iterable[AbstractModelRepository] = (BiGGModels(), BioModels()), cache: bool = True) → '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