'retropath2 sink generator'
Project description
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
Project details
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