https://github.com/brsynth/rrparser

Reaction rules parser
https://github.com/brsynth/rrparser

Last synced: 8 months ago
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Reaction rules parser

• Host: GitHub
• URL: https://github.com/brsynth/rrparser
• Owner: brsynth
• License: mit
• Created: 2020-07-02T08:53:24.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2025-03-31T09:48:29.000Z (about 1 year ago)
• Last Synced: 2025-10-21T19:59:05.766Z (8 months ago)
• Language: Python
• Homepage:
• Size: 357 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# rrparser

Reaction Rules Parser

| Name | Downloads | Version | Platforms |

| --- | --- | --- | --- |

| [![Conda Recipe](https://img.shields.io/badge/recipe-rrparser-green.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) | 

[![Qodana](https://github.com/brsynth/RRParser/actions/workflows/code_quality.yml/badge.svg)](https://github.com/brsynth/RRParser/actions/workflows/code_quality.yml) [![Tests](https://github.com/brsynth/RRParser/actions/workflows/test.yml/badge.svg)](https://github.com/brsynth/RRParser/actions/workflows/test.yml)

## Description

*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

* **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.

* **input-format**: (string) Valid options: csv, tsv. Format of the input file

* **rule-type**: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction

* **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

## Install

### From Conda

```sh

[sudo] conda install -c conda-forge rrparser

```

## Use

### Function call from Python code

```python

from rrparser import parse_rules

outfile = parse_rules(

  ,

  ,

  input_format=<'csv' | 'tsv'>,

  rule_type=<'all' | 'retro' | 'forward'>,

  diameters=<'2,4,6,8,10,12,14,16'>,

  output_format=<'csv' | 'tsv'>

)

```

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 \

  rules-file  \

  [--input-format {csv,tsv}] \

  [--rule-type {all,retro,forward}] \

  [--outfile ] \

  [--diameters {2,4,6,8,10,12,14,16}] \

  [--output-format {csv,tsv}]

```

If `rules_files` is set to `retrorules`, RetroRules are fetched from `retrorules.org` and considered as input file.

## Tests

Test can be run with the following commands:

### Natively

```bash

python -m pytest -v

```

# CI/CD

For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).

## Authors

* **Joan Hérisson**

* Melchior du Lac

* Thomas Duigou

## 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.