fastq_download.py

import subprocess

sra_numbers = [
    "SRR7179504", "SRR7179505", "SRR7179506", "SRR7179507",
    "SRR7179508", "SRR7179509", "SRR7179510", "SRR7179511",
    "SRR7179520", "SRR7179521", "SRR7179522", "SRR7179523",
    "SRR7179524", "SRR7179525", "SRR7179526", "SRR7179527",
    "SRR7179536", "SRR7179537", "SRR7179540","SRR7179541"
    ]

# this will download the .sra files to ~/ncbi/public/sra/ (will create directory if not present)
for sra_id in sra_numbers:
    print ("Currently downloading: " + sra_id)
    prefetch = "prefetch " + sra_id
    print ("The command used was: " + prefetch)
    subprocess.call(prefetch, shell=True)

# this will extract the .sra files from above into a folder named 'fastq'
for sra_id in sra_numbers:
    print ("Generating fastq for: " + sra_id)
    fastq_dump = "fastq-dump --outdir fastq --gzip --skip-technical  --readids --read-filter pass --dumpbase --split-3 --clip ~/ncbi/public/sra/" + sra_id + ".sra"
    print ("The command used was: " + fastq_dump)
    subprocess.call(fastq_dump, shell=True)