RRParser

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

Input

• rules-file: (string) Filename of reaction rules
• 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
• 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

[sudo] python -m pip install rrparser

From Conda

[sudo] conda install -c brsynth rrparser

Use

Function call from Python code

from rrparser import Parser

outfile = Parser().parse_rules(rule_type, outdir, diameters)

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.main \
  [--rules-file <filename>] \
  [--input-format {csv,tsv}] \
  [--rule-type {all,retro,forward}] \
  --output <folder> \
  [--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 - 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.