Extract valid data from broken fastq file.

broken_fastq.py

def is_valid_fastq(lines):
    start = lines[0].startswith('@')
    middle = lines[2].startswith('+')
    length = len(lines[1]) == len(lines[3])
    return all([start, middle, length])

def FastqIterator(file):
    lines = [file.next(), file.next(), file.next()]
    for line in file:
        lines.append(line)
        if is_valid_fastq(lines):
            yield ''.join(lines)
        lines = lines[1:]

if __name__ == '__main__':
    import sys
    for record in FastqIterator(sys.stdin):
        sys.stdout.write(record)

Refer to 손상된 압축 FASTQ 파일의 손상부분 제거하기 and falsetru's improvement https://gist.github.com/falsetru/5435949