repair-fastq.py

import collections
import sys

def is_valid_fastq(lines):
    return (
        lines[0].startswith('@') and
        lines[2].startswith('+') and
        len(lines[1]) == len(lines[3])
    )

def FastqIterator(f):
    lines = collections.deque([next(f) for _ in range(3)], maxlen=4)
    for line in f:
        lines.append(line)
        if is_valid_fastq(lines):
            #yield from lines
            for line in lines:
                yield line

if __name__ == '__main__':
    sys.stdout.writelines(FastqIterator(sys.stdin))