Metadata-Version: 2.1
Name: rpextractsink
Version: 1.0.1
Summary: 'retropath2 sink generator'
Home-page: https://github.com/brsynth/rpextractsink
Author: 'melchior du lac, thomas duigou, joan hérisson'
Author-email: thomas.duigou@inra.fr
License: MIT
Description: # rpextractsink
        
        [![Anaconda-Server Badge](https://anaconda.org/brsynth/test/badges/latest_release_date.svg)](https://anaconda.org/brsynth/test) ![Test](https://github.com/brsynth/test/workflows/Test/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/brsynth/test/badges/version.svg)](https://anaconda.org/brsynth/test)
        
        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
        ```sh
        [sudo] python -m pip install rpextractsink
        ```
        ### From Conda
        ```sh
        [sudo] conda install -c brsynth rpextractsink
        ```
        
        ## Use
        
        ### Function call from Python code
        ```python
        from rpextractsink import rpextractsink
        
        TO_FILL
        ```
        
        If parameters from CLI have to be parsed, the function `build_args_parser` is available:
        ```python
        from TO_FILL import build_args_parser
        
        parser = buildparser()
        params = parser.parse_args()
        ```
        
        ### Run from CLI
        ```sh
        python -m rpextractsink
        ```
        
        
        ## Authors
        
        * **Melchior du Lac**
        * Thomas Duigou, Joan Hérisson
        
        ## License
        
        This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
        
        ### How to cite RetroRules?
        Please cite:
        
        TO_FILL
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/markdown
