生信软件13 - 基于sambamba 窗口reads计数和平均覆盖度统计

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Sambamba是一个高性能，高度并行，健壮和快速的工具（和库），用D编程语言编写，用于处理SAM和BAM文件。与samtools相比，其优势在于并行BAM读和写。

conda安装

conda install sambamba -y# github: https://github.com/biod/sambamba

基本用法

# 创建.bai index
samtools index sample.bam# 计算窗口reads数和平均覆盖度
sambamba depth window -w 1000 sample.sorted.bam > /path/sample.bam_read_depths.txt

统计结果

窗口reads计数的Python封装

参数输入：bam文件绝对路径

调用命令

python reads_depth.py -b /path/Sample.sorted.bam

主程序

# reads_depth.py
import os
import optparse
from pathlib import Pathclass ReadsDepth(object):def __init__(self, bam_path: str, window_size: int) -> None:path_obj = Path(bam_path)self.result_dir_path = path_obj.parentself.bam_path = bam_pathself.window_size = window_sizeself.sample_name = str(path_obj.stem).split('.')[0]self.output_path = os.path.join(self.result_dir_path, self.sample_name + '.bam_reads_depths.txt')self.bam_index()self.reads_depth()def bam_index(self):if not os.path.exists(self.bam_path + '.bai'):os.system("samtools index {}".format(self.bam_path))def reads_depth(self):run_status = os.system("sambamba depth window -w {0} {1} > {2}".format(self.window_size, self.bam_path, self.output_path))if __name__ == '__main__':parser = optparse.OptionParser(usage='"%prog"', version="%prog V1.0")parser.add_option("-b", "--bam-path", dest="bam_path", type=str, help="")parser.add_option("-w", "--window-size", dest="window_size", type=int, default=1000, help="bp")options, args = parser.parse_args()reads_depth = ReadsDepth(bam_path=options.bam_path, window_size=options.window_size)