bam.py 文件源码

def sort_by_name(file_name, sorted_prefix=None):
    """ Sorts a bam file by the read name, for paired-end
    """
    if sorted_prefix is None:
        sorted_prefix = file_name.replace('.bam', '') + '_namesorted'

    sorted_name = sorted_prefix + '.bam'
    # NOTE -- need to update our internal samtools in order to use pysam.sort
    #pysam.sort('-n', file_name, sorted_prefix)
    subprocess.check_call(['samtools', 'sort', '-n', file_name, sorted_prefix])

    return pysam.Samfile(sorted_name, 'rb')