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'retropath2 sink generator'

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RetroPath2 sink generator



  • input_sbml: (string) Path to the input SBML file


  • --remove_dead_end: (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
  • --compartment_id: (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files


  • output_sbml: (string) Path to the output csv file


From pip

[sudo] python -m pip install rpextractsink

From Conda

[sudo] conda install -c brsynth rpextractsink


Function call from Python code

from rpextractsink import rpextractsink


If parameters from CLI have to be parsed, the function build_args_parser is available:

from TO_FILL import build_args_parser

parser = buildparser()
params = parser.parse_args()

Run from CLI

python -m rpextractsink


  • Melchior du Lac
  • Thomas Duigou, Joan Hérisson


This project is licensed under the MIT License - see the LICENSE file for details

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