/extractor_brendapy

Primary LanguagePython

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