5.1.2.1.2. cobramod.parsing.bigg

Data parsing for BiGG

This module handles the retrieval of data from BiGG into a local directory. The possible type of data that can be download:

  • Metabolites: Normally, simple names.

  • Reactions: Mostly abbreviations.

  • Genes: It is included in the Reactions. Names and gene-reaction-rule is also

acquired

They change identifiers depending on the model given. BiGG have multiple models. Contact maintainers if other types should be added.

Important class of the module: - BiggParser: Child of the abstract class cobramod.parsing.base.BaseParser.

5.1.2.1.2.1. Module Contents

5.1.2.1.2.1.1. Classes

BiggParser

Helper class that provides a standard way to create an ABC using

5.1.2.1.2.1.2. Functions

retrieve_data(directory: pathlib.Path, identifier: str, model_id: str) → dict

Searchs in given parent directory if data is located in their respective
cobramod.parsing.bigg.retrieve_data(directory: pathlib.Path, identifier: str, model_id: str) → dict

Searchs in given parent directory if data is located in their respective model_id directory. Else, data will be retrieved from the corresponding model identifier. Returns dictionary from JSON.

Parameters

  • directory (Path) – Path to directory where data is located.

  • identifier (str) – Identifier for given database.

  • model_id (str) – Identifier of model for BiGG. Examples: e_coli_core, universal. Check http://bigg.ucsd.edu/models for a complete list of models.

Raises

  • HTTPError – If object is not available in given database

  • NotADirectoryError – If parent directory is not found

Returns

directory transformed from a JSON.

Return type

dict

class cobramod.parsing.bigg.BiggParser

Bases: cobramod.parsing.base.BaseParser

Helper class that provides a standard way to create an ABC using inheritance.