Metadata-Version: 2.1
Name: rrparser
Version: 1.1.8
Summary: Reaction Rules Parser
Home-page: https://github.com/brsynth/RRulesParser
Author: Thomas Duigou, Melchior du Lac, Joan Hérisson
Author-email: joan.herisson@univ-evry.fr
License: MIT
Description: # RRParser
        
        ![Test](https://github.com/brsynth/RRulesParser/workflows/Test/badge.svg) ![Publish](https://github.com/brsynth/RRulesParser/workflows/Publish/badge.svg)
        
        Reaction Rules Parser. If no input reaction files is provided, retrieves the reaction rules from [RetroRules](https://retrorules.org).
        
        ## Input
        
        * **rules-file**: (string) Filename of reaction rules
        * **rule-type**: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction
        * **outdir**: (string) Path where output files will be written
        * **diameters**: (integer list) Valid options: 2, 4, 6, 8, 10, 12, 14, 16. The diameter of the rules to return
        * **output-format**: (string) Valid options: csv, tar.gz. Format of the returned file
        
        ## Ouput
        
        * **output**: (string): Path of the output file. Either a compressed tar.gz (containing a csv) or csv list of reaction rules that are in a RetroPath2.0 friendly format
        
        
        ## Install
        ### From pip
        ```sh
        [sudo] python -m pip install rrparser
        ```
        ### From Conda
        ```sh
        [sudo] conda install -c brsynth rrparser
        ```
        
        ## Use
        
        ### Function call from Python code
        ```python
        from rrparser import Parser
        
        outfile = Parser().parse_rules(rule_type, outdir, diameters)
        ```
        
        If parameters from CLI have to be parsed, the function `build_args_parser` is available:
        ```python
        from rrparser import build_args_parser
        
        parser = buildparser()
        params = parser.parse_args()
        ```
        
        ### Run from CLI
        ```sh
        python -m rrparser.main \
          [--rules-file <filename>] \
          [--rule-type {all,retro,forward}] \
          --output <folder> \
          [--diameters {2,4,6,8,10,12,14,16}] \
          --output-format {csv,tar.gz}
        ```
        
        
        ## Authors
        
        * **Thomas Duigou**
        * Melchior du Lac
        * Joan Hérisson
        
        ## License
        
        This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
        
        ### How to cite RetroRules?
        Please cite:
        
        Duigou, Thomas, et al. "RetroRules: a database of reaction rules for engineering biology." Nucleic acids research 47.D1 (2019): D1229-D1235.
        
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
