rpextractsink 1.0.1

'retropath2 sink generator'

rpextractsink

RetroPath2 sink generator

Input

Required:

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

Optional:

• --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

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

Install

From pip

[sudo] python -m pip install rpextractsink

From Conda

[sudo] conda install -c brsynth rpextractsink

Use

Function call from Python code

from rpextractsink import rpextractsink

TO_FILL

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

Authors

• Melchior du Lac
• Thomas Duigou, Joan Hérisson

License

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

How to cite RetroRules?

Please cite:

TO_FILL