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 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.

Install

conda install -c conda-forge rp2biosensor

Run

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:

python -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output --otype dir

The 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.

Example

python -m rp2biosensor tests/data/input/rp2-results_lactate.csv --opath ./biosensor.html

For developpers

Install

conda env create -f environment.yaml -n rp2biosensor-dev
conda develop -n rp2biosensor-dev .

Test

python -m pytest -vv

Authors

• Thomas Duigou (tduigou)

Licence

rp2biosensor is released under the MIT licence. See the LICENSE.md file for details.