Metadata-Version: 2.1
Name: rrparser
Version: 1.1.6
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| |Publish|
        
        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
        ~~~~~~~~
        
        .. code:: sh
        
            [sudo] python -m pip install rrparser
        
        From Conda
        ~~~~~~~~~~
        
        .. code:: sh
        
            [sudo] conda install -c brsynth rrparser
        
        Use
        ---
        
        Function call from Python code
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from rrparser import Parser
        
            outfile = Parser().parse_rules(rule_type,
                                           rules_file,
                                           diameters,
                                           outdir,
                                           outfile,
                                           output_format)
        
        If parameters from CLI have to be parsed, the function
        ``build_args_parser`` is available:
        
        .. code:: python
        
            from rrparser import build_args_parser
        
            parser = buildparser()
            params = parser.parse_args()
        
        Run from CLI
        ~~~~~~~~~~~~
        
        .. code:: sh
        
            python -m rrparser \
              [--rules-file <filename>] \
              [--rule-type {all,retro,forward}] \
              [--outdir <folder>] \
              [--outfile <file>] \
              [--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.
        
        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.
        
        .. |Test| image:: https://github.com/brsynth/RRulesParser/workflows/Test/badge.svg
        .. |Publish| image:: https://github.com/brsynth/RRulesParser/workflows/Publish/badge.svg
        
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
