使用Snakemake批量合并样本染色体文件的技术实现问询

需求说明 #

需要对sample1至sample4共4个样本，分别合并每个样本对应的chr1、chrX、chrM三个独立文件，最终生成以下指定路径的合并文件：

result/sample1_merged_chr1XM.txt
result/sample2_merged_chr1XM.txt
result/sample3_merged_chr1XM.txt
result/sample4_merged_chr1XM.txt

手动合并命令示例 #

（注：原示例存在笔误，已修正为对应样本的chr1文件）

cat dirToFiles/sample1_chr_1_data.txt dirToFiles/sample1_chr_X_data.txt dirToFiles/sample1_chr_M_data.txt > result/sample1_merged.txt
cat dirToFiles/sample2_chr_1_data.txt dirToFiles/sample2_chr_X_data.txt dirToFiles/sample2_chr_M_data.txt > result/sample2_merged.txt
cat dirToFiles/sample3_chr_1_data.txt dirToFiles/sample3_chr_X_data.txt dirToFiles/sample3_chr_M_data.txt > result/sample3_merged.txt
cat dirToFiles/sample4_chr_1_data.txt dirToFiles/sample4_chr_X_data.txt dirToFiles/sample4_chr_M_data.txt > result/sample4_merged.txt

可复现代码（生成测试文件+Snakemake规则） #

步骤1：生成待合并的测试文件 #

用于创建模拟的样本染色体文件，方便验证合并逻辑：

#######################################
#Step 1: 创建待合并的多个文件
######################################

import subprocess
subprocess.run((['mkdir','-p', 'dirToFiles']))

SAMPLES = ["sample1", "sample2", "sample3", "sample4"]
CHROMS=["1", "X", "M"]

for sample in SAMPLES:
    for chrom in CHROMS:
        subprocess.run((['touch', f'dirToFiles/{sample}_chr_{chrom}_data.txt']))
        # 原代码中这条echo命令写法有误，无法正常写入内容，已注释

for sample in SAMPLES:
    for chrom in CHROMS:
        f = open(f'dirToFiles/{sample}_chr_{chrom}_data.txt', "w")
        f.write(f'dirToFiles/{sample}_chr_{chrom}_data.txt')
        f.close()

# 也可使用Snakemake的expand语法批量生成文件路径：
# expand("dirToFiles/{sample}_chr_{chrom}_data.txt", sample=SAMPLES, chrom=CHROMS)

步骤2：Snakemake规则编写 #

通过Snakemake实现批量自动化合并：

#################################
#Step 2: Snakemake 规则
#################################
SAMPLES = ["sample1", "sample2", "sample3", "sample4"]
CHROMS = ["1", "X", "M"]

rule all:
    input: expand("result/{sample}_merged_chr1XM.txt", sample=SAMPLES)


rule combineFiles:
    input:
        expand("dirToFiles/{sample}_chr_{chrom}_data.txt", chrom=CHROMS, partial=True)
    output:
        "result/{sample}_merged_chr1XM.txt"
    log: 
        "logs/{sample}_merged_chr1XM.txt"
    shell:
       """
cat {input} > {output} &> {log}
       """

内容的提问来源于stack exchange，提问作者sahuno