python split Sam文件的cigar

你可以使用pysam库来处理SAM文件并拆分CIGAR字段。下面是一个示例代码：

import pysam

def split_cigar(sam_file):
    sam = pysam.AlignmentFile(sam_file, "r")

    for read in sam.fetch():
        cigar_tuples = read.cigartuples
        if cigar_tuples is None:
            continue

        for cigar in cigar_tuples:
            operation, length = cigar

            if operation == 0:  # M (匹配)
                print(f"{length} bases matched")
            elif operation == 1:  # I (插入)
                print(f"{length} bases inserted")
            elif operation == 2:  # D (删除)
                print(f"{length} bases deleted")
            elif operation == 3:  # N (跳过)
                print(f"{length} bases skipped")
            elif operation == 4:  # S (软裁剪)
                print(f"{length} bases soft-clipped")
            elif operation == 5:  # H (硬裁剪)
                print(f"{length} bases hard-clipped")
            elif operation == 6:  # P (填充)
                print(f"{length} bases padded")
            elif operation == 7:  # = (相等的匹配)
                print(f"{length} bases equal")
            elif operation == 8:  # X (不相等的匹配)
                print(f"{length} bases mismatched")

    sam.close()

# 使用示例
sam_file = "your_sam_file.sam"
split_cigar(sam_file)

这段代码将打开指定的SAM文件，逐行读取每个比对，并分析其CIGAR字段，然后根据操作类型和长度进行打印输出。你可以根据自己的需求修改代码，以便进一步处理CIGAR字段的信息。