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If no input reaction files is provided, retrieves the reaction rules from [RetroRules](https://retrorules.org).\n\n## Input\n\n* **rules-file**: (string) Filename of reaction rules\n* **outfile**: (string) Filename containing the result of the parsing. If not set, result is printed out in the console. If ends with '.gz', it will be gzipped.\n* **input-format**: (string) Valid options: csv, tsv. Format of the input file\n* **rule-type**: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction\n* **diameters**: (integer list) Valid options: 2, 4, 6, 8, 10, 12, 14, 16. The diameter of the rules to return\n* **output-format**: (string) Valid options: csv, tar.gz. Format of the returned file\n\n\n## Install\n### From Conda\n```sh\n[sudo] conda install -c conda-forge rrparser\n```\n\n## Use\n\n### Function call from Python code\n```python\nfrom rrparser import parse_rules\n\noutfile = parse_rules(\n  \u003crules_file\u003e,\n  \u003coutfile\u003e,\n  input_format=\u003c'csv' | 'tsv'\u003e,\n  rule_type=\u003c'all' | 'retro' | 'forward'\u003e,\n  diameters=\u003c'2,4,6,8,10,12,14,16'\u003e,\n  output_format=\u003c'csv' | 'tsv'\u003e\n)\n```\n\nIf parameters from CLI have to be parsed, the function `build_args_parser` is available:\n```python\nfrom rrparser import build_args_parser\n\nparser = buildparser()\nparams = parser.parse_args()\n```\n\n### Run from CLI\n```sh\npython -m rrparser \\\n  rules-file \u003cfilename\u003e \\\n  [--input-format {csv,tsv}] \\\n  [--rule-type {all,retro,forward}] \\\n  [--outfile \u003cfilename\u003e] \\\n  [--diameters {2,4,6,8,10,12,14,16}] \\\n  [--output-format {csv,tsv}]\n```\nIf `rules_files` is set to `retrorules`, RetroRules are fetched from `retrorules.org` and considered as input file.\n\n## Tests\nTest can be run with the following commands:\n\n### Natively\n```bash\npython -m pytest -v\n```\n\n# CI/CD\nFor further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).\n\n## Authors\n\n* **Joan Hérisson**\n* Melchior du Lac\n* Thomas Duigou\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details\n\n### How to cite RetroRules?\nPlease cite:\n\nDuigou, Thomas, et al. \"RetroRules: a database of reaction rules for engineering biology.\" Nucleic acids research 47.D1 (2019): D1229-D1235.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frrparser","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Frrparser","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frrparser/lists"}