Use itertools.groupby to read a fastq file

yieldFastqRecord.py

def yieldFastqRecord (fh):
    """ a generator that yields a tuple of (fastq_readname, sequence, qualstring)
    adapted from this http://www.biostars.org/p/67246/#67556
    yields a tuple with (header_name,sequence)
    See http://freshfoo.com/blog/itertools_groupby """

    fqiter=(x[1] for x in itertools.groupby(fh, lambda line: line[0] == '@'))
    #fqiter is made of sub-iterators

    #the first sub-iter is the header
    for header in fqiter:
        readname=header.next().strip()
        #then the next sub-iters are sequence, '+', and qual
        #we concat them into a single string, then split them by '+'
        (sequence,quals)="".join(s.strip() for s in fqiter.next()).split("+")
        #finally we yield
        yield readname,sequence,quals
        

for  header,seq,qual in yieldFastqRecord(fh):
    print header
    print seq
    print qual

A qual string may contain '@'. This will cause the program trouble.