Hi,
I have a fastq.gz file and one of the read is causing problem with the alignment. I want to remove the read. I tried the following code but still no success. Have any one used any tools of which can handle the bad reads.
#!/usr/bin/env python
import sys
import gzip
def test():
f = sys.stdin
lastname = ''
i=0
minread = None
try:
while True:
lastname = ''
name = f.next().strip()
seq = f.next().strip()
plus = f.next().strip()
qual = f.next().strip()
i += 4
if name == '@D93Z3NS1:147:C3KT5ACXX:1:2216:13222:14536 D93Z3NS1:147:C3KT5ACXX:1:2216:13222:14536':
continue
print '%s\n%s\n+\n%s\n'%(name,seq,qual)
except:
pass
if __name__ == '__main__':
test()
Thanks,
Thank you for your reply. I tried the above linux cmd code and it does not work
Thanks,
Diya
you did it wrong or, that's a PATH problem, or your linux is missing the core utilities (!!!!!!) http://en.wikipedia.org/wiki/GNU_Core_Utilities