Catalytic project

model_catalytic.py is a script adding informations into an sbml model such as KEGG ID and genes names, and preprocessing data of the model to create lists taken as argument for km and kcat predictions

Requirements

Usage

python3 code/model_catalytic.py -m <sbmlmodel> -i -g -d <dataset> -k -c

Required argument

• -m, --model <sbmlmodel> : Metabolic model in sbml format.

Optional arguments

• -i, --keggid : Option to add kegg id in the model. Requires to add a dataset with option --data.

• -g, --genename : Option to add gene's name in the model. Requires to add a dataset with option --data.

• -d, --data <dataset> : Csv file containing colums of:

  • reaction's name in the model
  • the corresponding KEGG ID
  • a list og associated genes

• -k, --km : Option to find parametes to calculates km.

• -c, --kcat : Option to find parametes to calculates kcat.