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Reaction Rules Parser

Project 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


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