The parameters of this wrapper class are an empty directory that constains a single query file from https://www.ebi.ac.uk/gwas/downloads/summary-statistics. The instance will then extract all available files corresponding to that query file and place it into the respective directory.
Project Goals:
The goal of this repos is to extract GWAS summary statistics such that the data can be easily streamlined into the sc-DRS pipeline for transcriptomics-genomics integration.
Notes:
HTTP Query Endpoint:
https://www.ebi.ac.uk/gwas/api/search
HTTP GWAS Summary Statistics Endpoint:
http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
Download Dependencies:
git clone [email protected]:irsyadadam/gwas-api.git
pip install -r requirements.txt
The following are the parameters for the API Wrapper:
usage: main.py [-h] [--folder FOLDER]
download all the gwas files given a gwas query from gwas catalog
optional arguments:
-h, --help show this help message and exit
--folder FOLDER folder to go through and see query file, should only have a csv in it
Example Usage:
The following command will search for the heart/ folder for a query file, and download all of the gwas files associated with the term "heart". This will only happen if the query file is searched with the term "heart".
python3 DOWNLOAD_GWAS.py --folder heart
The final GWAS summary statistics should be in the following format:
CHR BP SNP P N
1 717587 rs144155419 0.453345 279949
1 740284 rs61770167 0.921906 282079
1 769223 rs60320384 0.059349 281744