GWAS-FTP-retriever

This github repo contains only a Python script designed to automate the download of Genome-Wide Association Study (GWAS) summary statistics from an FTP server of NHGRI-EBI GWAS catalog. The script is particularly useful for downloading data related to specific study accessions from the GWAS catalog hosted by the European Bioinformatics Institute (EBI).

Made by Ho Vu Hoang Khoa

Installation:

Directly download the script or you can do the fancy way git clone this repo.

Usage:

python FTP_retriever_advanced.py <Accession number 1> <Accession number 2> ...

Workflow

Features

• Automated FTP Connection: Establishes an anonymous FTP connection to the EBI GWAS server.
• Recursive Directory Download: Supports downloading entire directories or individual files recursively from the FTP server.
• Robust Error Handling: Implements retry logic with exponential backoff for handling temporary errors during FTP operations.
• Colored Console Output: Uses colorama for color-coded messages in the terminal, enhancing readability of the process.
• Beautiful progressbar: Display a progressbar from tqdm to show the download progress.
• Download Time Tracking: Measures and displays the time taken for each download.

Requirements

• Python 3.x
• The following Python packages:
  • ftplib
  • tqdm
  • colorama

You can install the required packages using pip:

pip install tqdm colorama