The companion querying tool for the IBDGC ID association database (https://github.com/ibdgc/ibdgc-db). Features of this application were forked from a subset of the ibdgc-db codebase for the sake of simplification. This allowed for the separation of the less restricted query access from the more restricted database provisioning. Functionality maintained here generally revolves around the lookup command.
The package should be installed from the source repo. Clone the repo, and execute the pip install. It's strongly encouraged that you use some type of environment management like venv or conda.
# setup your env (venv/conda)
# clone the repo
git clone https://github.com/ibdgc/id-search.git
# install from the project root
cd id-search
pip install .
This tool requires the presence of the ibdgc.db database. The database is rebuilt weekly and can be found in the IBDGC OSF Collection as a component of the ID Tracking project. Access to this database is restricted to IBDGC members and collaborators. Access can be requested at the OSF project link below. Please contact the DCC for clarifications on access (contact@ibdgc.org).
- Download the ID database found at this project component: (https://osf.io/gmnfk/)
- Place the database in the
tmpdirectory under the id-search project root
mv ibdgc.db id-search/tmp
UNDER DEVELOPMENT
The search tool contains a lookup function which offers a preconfigured query of the database by ID. Queries can be made in a batch fashion that will generate a dataframe output. This is automatically written to a csv file in the project tmp directory.
This is a basic search by NIDDK consortium ID.
id-search lookup A269801-131080
This query is an example of how to search by GWAS Mega 2 project GM IDs.
id-search lookup -i genotyping_result.id GM211-1694