Reaction Rules Parser
Project description
RRulesParser
Reaction Rules Parser. If no input reaction files is provided, retrieves the reaction rules from RetroRules.
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
[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,
rules_file,
diameters,
outdir,
outfile,
output_format)
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>] \
[--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 - 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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
rrparser-1.0.8.tar.gz
(4.7 kB
view hashes)