https://github.com/brsynth/rp2biosensor
Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output
https://github.com/brsynth/rp2biosensor
synbio synthetic-biology
Last synced: 4 months ago
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Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output
- Host: GitHub
- URL: https://github.com/brsynth/rp2biosensor
- Owner: brsynth
- License: mit
- Created: 2021-12-14T16:03:16.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-01-03T14:13:33.000Z (over 3 years ago)
- Last Synced: 2025-10-21T19:56:47.542Z (8 months ago)
- Topics: synbio, synthetic-biology
- Language: HTML
- Size: 575 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
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README
# rp2biosensor -- Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output
rp2biosensor extracts metabolic paths linking undetectable compounds
into a detectable one using biochemical reactions. This concept is known
as "Sensing-Enabling Metabolic Pathways". See [doi: 10.1021/acssynbio.5b00225](https://doi.org/10.1021/acssynbio.5b00225)
for more.
In short, rp2bionsensor converts the output of [RetroPath2.0](https://www.myexperiment.org/workflows/4987.html) into a HTML page showing the possible metabolic paths linking the compound to be detected to the detectable ones.
Notice: only the shortest paths are kept. This mean that if there is a 1 step path, no 2 steps will be outputted.
## Install
```bash
conda install -c conda-forge rp2biosensor
```
## Run
```bash
python -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output/file.html --otype file
```
By default, all the needed dependancies are embedded into the HTML file. This includes CSS, JavaScript, and data files. Alternatively, the output could be outputted into a directory, using the `dir` output type:
```bash
python -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output --otype dir
```
The embedded help:
```bash
python -m rp2biosensor -h
usage: rp2biosensor [-h] [--opath OPATH] [--otype {dir,file}] [--ojson OJSON] [--cache-dir CACHE_DIR] rp2_results sink_file
Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.
positional arguments:
rp2_results RetroPath2.0 results
sink_file Sink file used for RetroPath2.0
options:
-h, --help show this help message and exit
--opath OPATH Output path. Default: /Users/tduigou/code/rp2biosensor/biosensor.html.
--otype {dir,file} Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file
--ojson OJSON Output the graph as json file if the path is not None. Default: None
--cache-dir CACHE_DIR
Path to the cache directory. If not specified, None is passed to rrCache.
```
## Example
```bash
python -m rp2biosensor tests/data/input/rp2-results_lactate.csv --opath ./biosensor.html
```
## For developpers
### Install
```bash
conda env create -f environment.yaml -n rp2biosensor-dev
conda develop -n rp2biosensor-dev .
```
### Test
```bash
python -m pytest -vv
```
## Authors
- Thomas Duigou ([tduigou](https://github.com/tduigou))
## Licence
rp2biosensor is released under the MIT licence. See the [LICENSE.md](LICENSE.md) file for details.