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 for more.
In short, rp2bionsensor converts the output of RetroPath2.0 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.
conda install -c conda-forge rp2biosensorpython -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output/file.html --otype fileBy 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:
python -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output --otype dirThe embedded help:
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.python -m rp2biosensor tests/data/input/rp2-results_lactate.csv --opath ./biosensor.htmlconda env create -f environment.yaml -n rp2biosensor-dev
conda develop -n rp2biosensor-dev .python -m pytest -vv- Thomas Duigou (tduigou)
rp2biosensor is released under the MIT licence. See the LICENSE.md file for details.