About

This repository builds a pyhthon:3.8-slim based docker container running the script in the folder src This script reads in the ini-files in the config folder and then proceeds to download pathway maps from the KEGG API.

The KEGG API has the following Restriction:

KEGG API is provided for academic use by academic users belonging to academic institutions.

If you are not an academic user belonging to an academic institution please contact KEGG to aquire a licence.

Building the image

After cloing the repository you can build the image with:

docker build -t kpwd .

Running the container

To run the container you need to have two local directories ready to be mounted in the container One of the directories is used to store the downloaded kgml files. The other is the location of the config files used by the python script.

Please find an example call below; edit to your preferences and system:

docker run -it --volume=${PWD}/data:/data --volume=${PWD}/config:/config kpwd examples/example.ids

Configuring the logger

To change the logging behaviour during execution use the file

config/logging-config.ini

Please refer to the official documentation for instructions. Most notably you might want to enable DEBUG output by changing the line

level=INFO

to

level=DEBUG

in case of errors.

Configuring the downloader

To change the behaviour of the downloader use the file

config/keggdownload-config.ini

The following sections are available

kegg_api

Change the content to be downloaded

action

The way KPWD handles the input is controlled by the

action

config option. It takes one of the following arguments:

all

The config setting

action= all

will attempt to download all pathway maps on the index. WARNING: This will download more than 200 pathways!

search

If

action= search

the first paramter to the python script (or the docker run command) will act as a search term for the KEGG pathways and will match all pathways, whose name contains the given search term.

list

This enables to provide a list of pathway map ids (including organsim code, or map'' prefix) in the map_ids'' option. Example:

action= list
map_ids= hsa05200,05223

file

This treats the first parameter to the python script as a file name in the config folder that contains the pathway ids that should be downloaded.

action= file

commandline

With

action=commandline

the arguments to the python script will be treated as pathway id that are attempted to be downloaded.

orgCode

Give a three letter organism code to download the maps for this organism. To get the maps for homo sapiens use:

hsa

If omitted the references maps are fetched.

container_env

Here you can configure the environment of your specific container setup. At the moment only the download folder can be configured. Open an Issue if you are in need of more configuration options.

download_folder

The standard folder inside the container to use and to map the volume to is

/data

but you change it if you need to use a different folder in the container. If you omit this setting, the default /data will be used.

No warranties

This tool comes without any warranties. Use at your own risk, I cannot be made liable for any damage to your hard- or software when using this program and to any breach of license you might infringe when using this program without a KEGG license. See below.

KEGG API Restriction

Just to be safe I will repeat the KEGG restriction here which applies to your use of this software:

Restriction:
KEGG API is provided for academic use by academic users belonging to academic institutions.

For more details please visit the KEGG website at [https://www.kegg.jp/kegg/rest/]