utils.py 文件源码

def get_unmapped_read_count_from_indexed_bam(bam_file_name):
    """
    Get number of unmapped reads from an indexed BAM file.

    Args:
        bam_file_name (str): Name of indexed BAM file.

    Returns:
        int: number of unmapped reads in the BAM

    Note:
        BAM must be indexed for lookup using samtools.

    """

    index_output = subprocess.check_output('samtools idxstats %s' % bam_file_name, shell=True)
    return int(index_output.strip().split('\n')[-1].split()[-1])