17.1.1.3.1.1.1.4. cobra.io.web.load
¶
Provide a function load_model
to access remote model repositories.
17.1.1.3.1.1.1.4.1. Module Contents¶
17.1.1.3.1.1.1.4.1.1. Functions¶
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Download an SBML model from a remote repository. |
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Attempt to load a gzip-compressed SBML document from the cache. |
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Attempt to load a gzip-compressed SBML document from the given repositories. |
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Generate a model instance from a gzip-compressed, UTF-8 encoded SBML document. |
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cobra.io.web.load.
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
BiGGModels()
,BioModels()
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cobra.io.web.load.
_cached_load
(model_id: str, repositories: Iterable[AbstractModelRepository]) → bytes[source]¶ Attempt to load a gzip-compressed SBML document from the cache.
If the given model identifier is not in the cache, the remote repositories are searched.
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cobra.io.web.load.
_fetch_model
(model_id: str, repositories: Iterable[AbstractModelRepository]) → bytes[source]¶ Attempt to load a gzip-compressed SBML document from the given repositories.