rrparser

Reaction Rules Parser

Name	Downloads	Version	Platforms

Description

Reaction Rules Parser. If no input reaction files is provided, retrieves the reaction rules from RetroRules.

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

[sudo] conda install -c conda-forge rrparser

Use

Function call from Python code

from rrparser import parse_rules

outfile = parse_rules(
  <rules_file>,
  <outfile>,
  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:

from rrparser import build_args_parser

parser = buildparser()
params = parser.parse_args()

Run from CLI

python -m rrparser \
  rules-file <filename> \
  [--input-format {csv,tsv}] \
  [--rule-type {all,retro,forward}] \
  [--outfile <filename>] \
  [--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

python -m pytest -v

CI/CD

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

Authors

• Joan Hérisson
• Melchior du Lac
• Thomas Duigou

License

This project is licensed under the MIT License - see the 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.