query_quickgo

This Python3 script builds URL requests for QuickGO API based on provided arguments, sends it to QuickGO, and processes the response.

How to install

Get the dependencies: Python (at least 3.8) and Python packages:

pip install pandas
pip install requests

Clone the repository

git clone https://github.com/IvanTsers/query_quickgo
cd query_quickgo

An example run:

python query_quickgo.py search -q respiration

There are eight subcommands: chart, swissprot, coterms, define, search, descendants, ancestors, and children. Help is available for every command.

Run using Docker

The script and all its dependencies can be containerized. To build your local copy of the image query_quickgo:

git clone https://github.com/IvanTsers/query_quickgo
cd query_quickgo
sudo docker build -t query_quickgo -f docker/Dockerfile --force-rm .

An example run:

sudo docker run --rm query_quickgo search -q respiration

To save charts generated by the container, redirect to a file (instead of using the -out argument):

sudo docker run --rm query_quickgo chart -ids GO:1903715 > chart.png