https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
sra_download.py
#!/usr/bin/python
import sys
from subprocess import call
print "sra_download.py ListOfSRAAccessionNumbers"
try:
li = sys.argv[1]
except:
li = raw_input("Introduce list of SRA Accession Numbers")
data = open(li).readlines()
for line in data:
acc = line[:-1]
url = "ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/%s/%s/%s/%s.sra" % (acc[0:3], acc[0:6], acc, acc)
print url
call("wget %s" % (url), shell = True)