Download script for 4dnuleome database

download_4dn.py

import os
import requests
from requests.auth import HTTPBasicAuth
import json
from tqdm.notebook import tqdm

def download_4dn(identifier, dowload_dir=os.getcwd(), pgbar=False):
    
    def download_file(url, dowload_dir=dowload_dir:
        if not os.path.exists(dowload_dir):
            os.makedirs(dowload_dir)
        file_name = url.split('/')[-1]
        with requests.get(url, stream=True) as r:
            r.raise_for_status()
            with open(file_name, 'wb') as f:
                if pgbar:
                    pbar = tqdm(total=int(r.headers['Content-Length']))
                for chunk in r.iter_content(chunk_size=8192):
                    if chunk:
                        f.write(chunk)         
                        if pgbar:
                            pbar.update(len(chunk))

    url = f"https://data.4dnucleome.org/ga4gh/drs/v1/objects/{identifier}/access/https"
    response = requests.get(url, auth=HTTPBasicAuth(key, secret))
    if not response.ok:
        assert 0
    info = response.json()    
    download_file(info["url"])

download_4dn('4DNFIA85JYD7')