Looks at a directory to try to find unpaired fastq files.
    :param fastq_directory: Complete path to directory containing fastq files.
    :param forward_id: Identifier for paired reads, forward.
    :param reverse_id: Identifier for paired reads, reverse.
    :return: List of paths to unpaired files.

def find_unpaired_reads(fastq_directory, forward_id='_R1', reverse_id='_R2'):
    """
    Looks at a directory to try to find unpaired fastq files.
    :param fastq_directory: Complete path to directory containing fastq files.
    :param forward_id: Identifier for paired reads, forward.
    :param reverse_id: Identifier for paired reads, reverse.
    :return: List of paths to unpaired files.
    """
    unpaired_list = list()
    fastq_files = glob.glob(os.path.join(fastq_directory, '*.f*q*'))
    for name in fastq_files:
        if forward_id not in name and reverse_id not in name:
            unpaired_list.append(name)
        elif forward_id in name and not os.path.isfile(name.replace(forward_id, reverse_id)):
            unpaired_list.append(name)
        elif reverse_id in name and not os.path.isfile(name.replace(reverse_id, forward_id)):
            unpaired_list.append(name)
    return unpaired_list