Reaction Rules Parser
Name | Downloads | Version | Platforms |
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Reaction Rules Parser. If no input reaction files is provided, retrieves the reaction rules from RetroRules.
- 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
[sudo] conda install -c conda-forge rrparser
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()
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.
Test can be run with the following commands:
python -m pytest -v
For further tests and development tools, a CI toolkit is provided in ci
folder (see ci/README.md).
- Joan HĂ©risson
- Melchior du Lac
- Thomas Duigou
This project is licensed under the MIT License - see the LICENSE file for details
Please cite:
Duigou, Thomas, et al. "RetroRules: a database of reaction rules for engineering biology." Nucleic acids research 47.D1 (2019): D1229-D1235.