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()