Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary
Keywords
Repository
RetroPath2.0 to pathways
Basic Info
Statistics
- Stars: 18
- Watchers: 2
- Forks: 10
- Open Issues: 0
- Releases: 10
Topics
Metadata Files
README.md
RP2paths -- RetroPath2.0 to pathways
RP2paths extracts the set of pathways that lies in a metabolic space file outputted by the RetroPath2.0 workflow. RetroPath2.0 is freely accessible on myExperiment.org at: https://www.myexperiment.org/workflows/4987.html.
Installation
From conda
```bash
installation in an already existing environment (see prerequisites)
conda activate
Usage
From CLI
Once a scope has been produced by RetroPath2.0, a typical command line for extracting the pathways from the results is
bash
python -m rp2paths all <retropath2_scope> [--outdir <outdir>]
where:
- all specify that all the tasks needed for retrieving pathways will be executed at once.
- <retropath2_scope> is the metabolic space outputted by the RetroPath2.0 workflow.
- --outdir <outdir> specify the directory in which all files will be outputted.
In the <outdir> folder, the complete set of pathways enumerated will be written in the out_paths.csv file. In addition, for each pathway there will be a .dot file (.dot representation of the graph) and a .svg file (.svg depiction of the pathway).
Available options
Additional options are described in the embedded help: ```
List of possible modes
python -m rp2paths -h
List of options for the all-in-one mode
python -m rp2paths all -h ```
Examples
Precomputed results (outputted by RetroPath2.0) are provided in the examples folder for few compounds (carotene, naringenin, pinocembrin, violacein).
Below are the command lines for generating pathways that lie in naringenin result file:
bash
source activate <myenv>
python -m rp2paths all examples/naringenin/rp2-results.csv --outdir examples/naringenin/outdir
No scope warnings
A warning message WARNING: *** Scope Task: no scope matrix was produced, exit indicates that no reaction have been indified as being part of a pathway. This can happen when the retrosynthesis exploration performed by RetroPath2.0 does not reach a minimal set of sink compounds.
For developers
Development installation
After a git clone:
bash
cd <repository>
conda env create -f environment.yaml -n <dev_env>
conda develop -n <dev_env> .
conda activate <dev_env>
Tests
Test can be run with the following commands:
Natively
bash
cd tests
pytest -v
CI/CD
For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).
How to cite RP2paths?
Please cite:
Delepine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002
Licence
RP2paths is released under the MIT licence. See the LICENCE.txt file for details.
Owner
- Name: BioRetroSynth
- Login: brsynth
- Kind: organization
- Website: http://www.jfaulon.com
- Repositories: 33
- Profile: https://github.com/brsynth
Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.
GitHub Events
Total
- Watch event: 2
- Push event: 3
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 2
- Push event: 3
- Fork event: 1
- Create event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| joan | j****n@u****r | 158 |
| Thomas Duigou | t****u@i****r | 48 |
| Thomas Duigou | t****u@i****r | 21 |
| Stian Soiland-Reyes | s****n@a****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 3
- Average time to close issues: 3 months
- Average time to close pull requests: 4 days
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 1.0
- Average comments per pull request: 0.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Melclic (2)
- Tryhood (1)
Pull Request Authors
- breakthewall (2)
- stain (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 20 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 4
- Total maintainers: 1
pypi.org: rp2paths
'retropath2.0 to pathways'
- Homepage: https://github.com/brsynth/rp2paths
- Documentation: https://rp2paths.readthedocs.io/
- License: MIT
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Latest release: 1.5.1
published over 5 years ago
Rankings
Maintainers (1)
conda-forge.org: rp2paths
- Homepage: https://github.com/brsynth/rp2paths
- License: MIT
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Latest release: 1.5.0
published about 4 years ago
Rankings
Dependencies
- graphviz
- lxml
- openjdk
- pandas
- pydotplus
- pytest
- python >=3.6
- python-graphviz
- rdkit 2019.03.1.0.*
- bandit * test
- flake8 * test
- pytest * test