Download sequence from NCBI SRA

download_sra.py

import os

#download SRA tool kit
def setup_sra_tool(url):
  !wget $url
  !gunzip sratoolkit.2.9.6-1-ubuntu64.tar.gz
  !tar -xf sratoolkit.2.9.6-1-ubuntu64.tar
  
  
#download SRA file and extract fastq
def get_sra(url, sra_path):
  os.chdir('/content')
  !wget $url
  sra_name = url[-11:]
  os.chdir(sra_path)
  !./fastq-dump /content/$sra_name -O /content/
  os.chdir('/content')
  
 
# url of SRA tool kit 
url_tk= 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/sratoolkit.2.9.6-1-ubuntu64.tar.gz'
setup_sra_tool(url_tk)

# example SRA file
sra_url = 'https://sra-download.ncbi.nlm.nih.gov/traces/era6/ERR/ERR3014/ERR3014700'
tool_path = '/content/sratoolkit.2.9.6-1-ubuntu64/bin'
get_sra(sra_url, tool_path)