5.1.1.1.6. `cobramod.core.retrieval`¶

Data retrieval

This module creates the function cobramod.core.retrieval.get_data(), which gets the data from a local directory or from different databases. The available databases for data retrieval can be found in the variable cobramod.core.retrieval.available_databases

5.1.1.1.6.1. Module Contents¶

Simple object that shows the information about the database

`get_data`(directory: pathlib.Path, identifier: str, database: str, debug_level: int = 20, **kwargs) → dict	Retrieves and transforms the data into a dictionary for the given
`translate`(directory: pathlib.Path, target: str, database: str) → str	Return the identifier of crossref for the given target. It can be a

`parsers`
`available_databases`

class cobramod.core.retrieval.Databases¶

Bases: object

Simple object that shows the information about the database

cobramod.core.retrieval.get_data(directory: pathlib.Path, identifier: str, database: str, debug_level: int = 20, **kwargs) → dict¶

Retrieves and transforms the data into a dictionary for the given identifier from a specific database.

Parameters

directory (Path) – Directory to store and retrieve local data.
identifier (str) – Original identifier.
database (str) – Name of database. Check cobramod.available_databases for a list of names.
debug_level (int, optional) – Level of debugging. Read package logging for more info. Defaults to 20.

Keyword Arguments

model_id – Exclusive for BIGG. Original identifier of the model to be searched. Some examples: “e_coli_core”, “universal”.
genome (str, optional) – Exclusive for KEGG. Abbreviation for the species involved. Genes will be obtained for this species.

Returns

Relevant data for the given identifier.

Return type

dict

cobramod.core.retrieval.translate(directory: pathlib.Path, target: str, database: str) → str¶

Return the identifier of crossref for the given target. It can be a metabolite or a Reaction.

Parameters

directory (Path) – Path of stored data.
target (str) – Identifier to search for.
database (str) – Pattern for the name of the cross-reference, e.g CAS, BIGG.