bam.py 文件源码

def sort_and_index(file_name, sorted_prefix=None):
    """ Sorts and indexes the bam file given by file_name.
    """
    if sorted_prefix is None:
        sorted_prefix = file_name.replace('.bam', '') + '_sorted'

    sorted_name = sorted_prefix + '.bam'
    subprocess.check_call(['samtools','sort', '-o', sorted_name, file_name])
    pysam.index(sorted_name)