brsynth / extractor_brendapy

Extractor BrendaPy

Extract the desired enzymatic data from Brenda using the brendapy parser. Here, we have chosen to store the datasets in json files.

Installation

git clone https://github.com/brsynth/extractor_brendapy.git
cd extractor_brendapy
conda env create -f environment.yaml -n <name_env>
conda activate <name_env>

Usage

The following 3 arguments are optional.

list_parameter : list of parameters below

path_files : path to the folder containing data_brenda.txt and file result json.

list_ec : if this argument is not set, list of all known ec is generated

In the terminal

python -m extractor_brendapy --list_parameters [PARAM1 PARAM2 ...] --path_file_databrenda [PATH] --list_ec [PARAM1 PARAM2 ...]

List of possible parameters :

ec; uniprot; organism; ID; substrate; value; comment; units; refs; data; chebi; KM; KKM; KI; TN; IC50; ref; TS; SY; SU; ST; SP; SA; PU; NSP; MW; LO; GI; IN; CL; CF; AP; tissues; SN; RT; RN; RE

Please note: When you want the parameters 'KM', 'KKM', 'KI', 'TN', 'IC50', you must add substrate to the list of requested elements.

For parameters: "ref", "TS", "SY", "SU", "ST", "SP", "SA", "PU", "NSP", "MW", "LO", "GI", "IN", "CL", "CF", "AP" add data.

Authors

• Nolwenn Paris
• Joan Hérisson

Licence