ebi_url_from_srr.py

#API created by @apfejes (Anthony Fejes) on top of my half-cooked script
#python ebi_url_from_srr.py --file srr_list.txt | xargs -I {} wget {}

import argparse
def prepareURL(srr_name, prefix="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/"):
    dir_1=srr_name[:6]
    dir_2=""
    url=""
    num_digits=sum(s.isdigit() for s in srr_name)
    if(num_digits == 6):
        url=prefix+dir_1+"/"+srr_name+"/"
    elif(num_digits == 7):
        dir_2="00"+srr_name[-1]
        url=prefix+dir_1+"/"+dir_2+"/"+srr_name+"/"
    elif(num_digits == 8):
        dir_2="0"+srr_name[-2:]
        url=prefix+dir_1+"/"+dir_2+"/"+srr_name+"/"
    elif(num_digits == 9):
        dir_2=srr_name[-3:]
        url=prefix+dir_1+"/"+dir_2+"/"+srr_name+"/"
    return url
def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('--SRR', help='SRR name to be parsed')
    parser.add_argument('--file', help='file containing SRR name to be parsed')
    args = parser.parse_args()
    if args.file:
        with open(args.file) as srr_file:
            for line in srr_file:
                url = prepareURL(line.strip())
                print("{}*.fastq.gz".format(url))
    else:
        url = prepareURL(args.SRR)
        print("{}*.fastq.gz".format(url))
if __name__ == '__main__':
    main()

check this gist as well https://gist.github.com/crazyhottommy/b9f6ee0122538b69876fad090cb7211b to understand how the fastqs are organized in the portal