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Open Source Science

https://github.com/brsynth/rrparser

Reaction rules parser

https://github.com/brsynth/rrparser

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Reaction rules parser

Basic Info
  • Host: GitHub
  • Owner: brsynth
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 357 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 10
Created almost 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

rrparser

Reaction Rules Parser | Name | Downloads | Version | Platforms | | --- | --- | --- | --- | | Conda Recipe | Conda Downloads | Conda Version | Conda Platforms |

Qodana Tests

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

sh [sudo] conda install -c conda-forge rrparser

Use

Function call from Python code

```python from rrparser import parse_rules

outfile = parserules( <rulesfile>, , inputformat=<'csv' | 'tsv'>, ruletype=<'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 buildargsparser

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

Run from CLI

sh 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

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).

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.

Owner

  • Name: BioRetroSynth
  • Login: brsynth
  • Kind: organization

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.

GitHub Events

Total
  • Release event: 2
  • Delete event: 1
  • Push event: 45
  • Pull request event: 1
  • Create event: 2
Last Year
  • Release event: 2
  • Delete event: 1
  • Push event: 45
  • Pull request event: 1
  • Create event: 2

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 382
  • Total Committers: 2
  • Avg Commits per committer: 191.0
  • Development Distribution Score (DDS): 0.005
Past Year
  • Commits: 28
  • Committers: 1
  • Avg Commits per committer: 28.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
joan j****n@u****r 380
kenza12 k****k@l****r 2
Committer Domains (Top 20 + Academic)
live.fr: 1 univ-evry.fr: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 35 minutes
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (2)
  • kenza12 (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
conda-forge.org: rrparser
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 59.3%
Average: 59.3%
Last synced: 10 months ago

Dependencies

.github/workflows/code_quality.yml actions
  • JetBrains/qodana-action v2022.3.4 composite
  • actions/checkout v3 composite
.github/workflows/tag.yml actions
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v2 composite
  • actions/upload-artifact v2 composite
  • ad-m/github-push-action master composite
  • conda-incubator/setup-miniconda v2 composite
  • mathieudutour/github-tag-action v5.6 composite
  • ruby/setup-ruby v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
environment.yaml pypi
setup.py pypi