7.1.1.3.1.1. 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 downloaded:

  • 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

7.1.1.3.1.1.1. Attributes

debug_log

7.1.1.3.1.1.2. Functions

find_url(model_id, query)

Tries to find a valid URL for the API of BIGG. It will return a

build_reference(json_data)

Return a dictionary of cross-references, where the keys are the

parse_reaction_attributes(data, entry)

parse_metabolite_attributes(data)

parse_genes(data, rule)

7.1.1.3.1.1.3. Module Contents

cobramod.parsing.bigg.debug_log
cobramod.parsing.bigg.find_url(model_id, query)

Tries to find a valid URL for the API of BIGG. It will return a requests.Response if URL is valid. object

Parameters:

  • model_id (str) – Name for the specific BIGG model identifier.

  • identifier (str) – Identifier for the item. Can be a reaction or compound

  • query (str)

Returns:

A valid request Response followed by the database

Version.

Return type:

(Response,str)

Raises:

HTTPError – If identifier is not found in BIGG database.

cobramod.parsing.bigg.build_reference(json_data)

Return a dictionary of cross-references, where the keys are the cross-references and values the their identifiers.

Parameters:

json_data (dict[str, Any])

Return type:

dict[str, str]

cobramod.parsing.bigg.parse_reaction_attributes(data, entry)
Parameters:
Return type:

dict[str, Any]

cobramod.parsing.bigg.parse_metabolite_attributes(data)
Parameters:

data (dict[str, Any])

Return type:

dict[str, Any]

cobramod.parsing.bigg.parse_genes(data, rule)
Parameters: