{"id":25220,"date":"2024-01-19T16:47:13","date_gmt":"2024-01-19T08:47:13","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25220"},"modified":"2024-01-19T16:47:15","modified_gmt":"2024-01-19T08:47:15","slug":"%e6%90%ad%e5%bb%ba%e7%94%9f%e4%bf%a1%e5%88%86%e6%9e%90%e6%b5%81%e6%b0%b4%e7%ba%bf%ef%bc%8c%e5%a6%82%e5%b7%a5%e5%8e%82%e4%b8%80%e6%a0%b724%e5%b0%8f%e6%97%b6%e6%98%bc%e5%a4%9c%e8%bf%90%e8%bd%ac","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25220","title":{"rendered":"\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u663c\u591c\u8fd0\u8f6c\u2014\u2014snakemake"},"content":{"rendered":"

<\/h1>\n

<\/p>\n

\u8fd8\u5728\u7528Shell\u811a\u672c\u8dd1\u751f\u4fe1\u6d41\u7a0b\u5417\uff1f\u5728\u4e3a\u4e2d\u65ad\u7684Shell\u811a\u672c\u641e\u5f97\u5d29\u6e83\u5417\uff1f\u4fee\u6539\u65e5\u79ef\u6708\u7d2f\u7684\u4ee3\u7801\u592a\u5934\u5927\uff1f<\/p>\n

\u90a3\u6709\u6ca1\u6709\u4ec0\u4e48\u529e\u6cd5\uff0c\u89e3\u51b3\u4e86\u4e0a\u9762\u7684\u7f3a\u70b9\uff0c\u80fd\u8ba9\u4eba\u5c11\u6389\u5934\u53d1\u5462\uff1f<\/p>\n

\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u63a8\u8350Snakemake\uff0c\u8ba9\u4f60\u7684\u751f\u4fe1\u5206\u6790\u6d41\u7a0b\uff0c \u50cf\u5de5\u5382\u7684\u6d41\u6c34\u7ebf\u4e00\u6837\u5f00\u52a8\u8d77\u6765\uff01<\/p>\n

Snakemake\u4e24\u4e2a\u7b80\u5355\u6848\u4f8b\u8ba9\u4f60\u4e00\u770b\u5c31\u61c2\u3002<\/p>\n

Snakemake\u662f\u4ec0\u4e48\uff1f<\/h3>\n

Snakemake\u662f\u4e00\u6b3e\u57fa\u4e8ePython3\u7684\u8f6f\u4ef6\uff0c\u4e3b\u8981\u80fd\u591f\u5e2e\u52a9\u7528\u6237\u5feb\u901f\u642d\u5efa\u9700\u8981\u91cd\u590d\u5b9e\u73b0\u7684\u5206\u6790\u6d41\u7a0b\u3002<\/p>\n

\u4ee5\u4e0b\u662f\u5b83\u7684\u5b98\u65b9\u6587\u6863\u3002<\/p>\n

Snakemake \u2014 Snakemake 7.30.1 documentation<\/a><\/p>\n

Snakemake\u7684\u4f18\u52bf<\/h2>\n
    \n
  1. \u901a\u8fc7treads\u53ef\u4ee5\u8bbe\u7f6e\u4efb\u52a1\u7684\u7ebf\u7a0b\u6570\u76ee\uff0c\u5b9e\u73b0\u5e76\u884c\u5904\u7406<\/li>\n
  2. \u4e2d\u65ad\u7684\u7a0b\u5e8f\uff0csnake\u53ef\u4ee5\u8bb0\u5f55\u4e0b\u6765\uff0c\u4ece\u65ad\u6389\u7684\u5730\u65b9\u7ee7\u7eed\u8fd0\u884c\uff08\u62ef\u6551\u4e86\u591a\u5c11\u751f\u4fe1\u4eba\uff09<\/li>\n
  3. \u56e0\u4e3a\u5176\u662f\u901a\u8fc7python3\u5f00\u53d1\u7684\uff0c\u53ef\u4ee5\u4f7f\u7528python\u5e93<\/li>\n
  4. \u652f\u6301shell\u547d\u4ee4\u64cd\u4f5c<\/li>\n
  5. \u81ea\u52a8\u751f\u6210\u6d41\u7a0b\u7684\u62d3\u6251\u56fe\uff0c\u4f7f\u4f60\u7684\u6d41\u7a0b\u4e00\u76ee\u4e86\u7136<\/li>\n<\/ol>\n

    \u4f8b\u5982\u50cf\u4e0b\u9762\u8fd9\u5f20\u6d41\u7a0b\u56fe\u4e00\u6837<\/p>\n

    \"IMG_256\"<\/p>\n

    \u7b2c\u4e00\u4e2a\u6848\u4f8b\uff1a\u5408\u5e76\u6587\u4ef6\u5165\u95e8Snakemake<\/h2>\n

    \u73af\u5883\u51c6\u5907<\/h3>\n

    \u63a8\u8350\u4f7f\u7528\u7248\u672c\u7ba1\u7406conda\u5b89\u88c5snakemake\u3002(mamba\u662fconda\u7684C++\u7248\u672c\u5176\u8fd0\u884c\u901f\u5ea6\u66f4\u5feb\uff0c\u4e0b\u8f7d\u66f4\u5feb\uff0c\u5982\u679c\u4f60\u8fd8\u4e0d\u77e5\u9053\uff0c\u8bf7\u5feb\u4e0b\u8f7d\u8bd5\u8bd5\u5427\uff0c\u4e00\u5b9a\u8ba9\u4f60\u7231\u4e0a\u5b83\u3002)<\/p>\n

    \u9996\u5148\u521b\u5efa\u865a\u62df\u73af\u5883\uff0c\u4e3a\u4e86\u6d41\u7a0b\u53ef\u590d\u73b0\uff0c\u6307\u5b9apython\u7248\u672c\u4e3a3.5\u3002<\/p>\n

    $ mamba create -n snake<\/p>\n

    $ conda activate snake<\/p>\n

    $ mamba install -y snakemake #\u4f7f\u7528mamba \u5b89\u88c5snakemake<\/p>\n

    \u7b80\u5355\u7684snakemake\u5b9e\u4f8b<\/h2>\n

    \u8fd9\u91cc\u4e3e\u4e00\u4e2a\u7b80\u5355\u6613\u61c2\u7684\u5408\u5e76\u6587\u4ef6\u5185\u5bb9\u7684\u4f8b\u5b50\uff0c\u5e2e\u52a9\u4f60\u5feb\u901f\u5165\u95e8snakemake<\/p>\n

    \u5148\u521b\u5efa\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff0c\u91cc\u9762\u7684\u5185\u5bb9\u4e3ahello\uff0c\u518d\u521b\u5efa\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff0c\u5185\u5bb9\u4e3aworld\u3002<\/p>\n

    $echo “hello” > hello.txt<\/p>\n

    $echo “world” > world.txt<\/p>\n

    \u63a5\u4e0b\u6765\u6211\u4eec\u5f00\u59cb\u7f16\u5199snakemake\u6d41\u7a0b\u6587\u4ef6snakefile<\/p>\n

    rule concat:<\/p>\n

    input:<\/p>\n

    expand(“{file}.txt”, file=[“hello”, “world”])<\/p>\n

    output:<\/p>\n

    “merged.txt”<\/p>\n

    shell:<\/p>\n

    “cat {input} > {output}”<\/p>\n

    concat\u662f\u4e3a\u8fd9\u4e2arule\u8d77\u7684\u540d\u5b57\u3002<\/p>\n

    input\u4e3a\u8f93\u5165\u7684\u6587\u4ef6\u3002<\/p>\n

    output\u4e3a\u8f93\u51fa\u7684\u6587\u4ef6\u3002<\/p>\n

    shell\u4e3a\u6267\u884c\u7684\u811a\u672c\u547d\u4ee4\u3002<\/p>\n

    {}\u7c7b\u4f3c\u4e8e\u901a\u914d\u7b26\uff0c\u901a\u8fc7expand\u4f1a\u901a\u914dfile=[“hello”, “world”]\u6587\u4ef6\u3002<\/p>\n

    \u5728\u540c\u4e00\u76ee\u5f55\u4e0b\u8fd0\u884csnakemake<\/p>\n

    \u5f53\u6267\u884c\u5de5\u4f5c\u6d41\u65f6\uff0cSnakemake\u4f1a\u5c1d\u8bd5\u751f\u6210\u7ed9\u5b9a\u7684\u76ee\u6807\u6587\u4ef6\u3002<\/p>\n

    $ snakemake<\/p>\n

    <\/p>\n

    \u8fd9\u6837\u8fd0\u884c\u5c31\u5b8c\u6210\u4e86\uff0c\u6211\u4eec\u6253\u5f00\u8f93\u51fa\u6587\u4ef6\u770b\u4e00\u4e0b<\/p>\n

    $ less merge.txt<\/p>\n

    <\/p>\n

    \u8fd9\u6837\u6587\u4ef6\u4e24\u4e2a\u6587\u4ef6\u5c31\u5408\u5e76\u6210\u4e00\u4e2a\u6587\u4ef6\u4e86\u3002<\/p>\n

    \u901a\u8fc7\u4e0a\u9762\u4e00\u4e2a\u5b9e\u4f8b\uff0c\u6211\u4eec\u80fd\u591f\u770b\u5230\u3002snakemake\u6d41\u7a0b\u7684\u57fa\u672c\u5355\u5143\u4e3arule, \u5728\u8fd9\u4e2arule\u91cc\u5206\u4e3a\u4e09\u90e8\u5206\u5185\u5bb9\uff0c\u7b2c\u4e00\u4e2a\u662finput\u8f93\u5165\u6587\u4ef6\uff0c\u7b2c\u4e8c\u4e2a\u662foutput\u8f93\u51fa\u6587\u4ef6\uff0c\u7b2c\u4e09\u4e2a\u662fsell\uff0c\u8fd0\u884c\u7684shell\u547d\u4ee4\uff08\u5c06shell\u6539\u4e3arun\uff0c\u5b83\u8fd8\u53ef\u4ee5\u8fd0\u884cpython\u6216R\u8bed\u8a00\u4ee3\u7801\uff09\u3002<\/p>\n

    snakemake\u7684\u6bcf\u4e00\u4e2arule\u5c31\u50cf\u5de5\u5382\u91cc\u7684\u4e00\u53f0\u673a\u5668\uff0c\u6211\u4eec\u901a\u8fc7\u4e0d\u65ad\u7684\u5c06\u8fd9\u4e9b\u673a\u5668\u4e32\u8054\u5728\u4e00\u8d77\uff0c\u5c31\u53ef\u4ee5\u7ec4\u88c5\u6210\u4e00\u6761\u751f\u4ea7\u7684\u6d41\u6c34\u7ebf\u4e86\u3002<\/p>\n

    \u7a7a\u8fd0\u884c<\/h3>\n

    \u63a5\u4e0b\u6765\u4ecb\u7ecd\u51e0\u4e2asnakemake \u5e38\u7528\u53c2\u6570:<\/p>\n

    –cores \u4e3a\u53ef\u4f9b\u7ed9\u6240\u6709\u4efb\u52a1\u7684\u603bcpu\u6838\u5fc3\u6570\u3002<\/p>\n

    -n\/–dry-run \u5219\u4e3a\u7a7a\u8fd0\u884c\uff0c\u53ea\u68c0\u67e5\u6240\u6709\u7684\u8f93\u5165\u8f93\u51fa\u5e76\u62a5\u544a\u9700\u8981\u6267\u884c\u7684\u4efb\u52a1\u6570\u3002\u4f46\u5e76\u4e0d\u771f\u6b63\u5730\u6267\u884c\u8ba1\u7b97\u811a\u672c\u3002<\/p>\n

    -p\/–printshellcmds \u8f93\u51fa\u6bcf\u4e00\u6b65\u7684shell\u547d\u4ee4\u3002<\/p>\n

    \u4fdd\u5b58\u5230Snakefile\u6587\u4ef6\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u8fdb\u884c\u7a7a\u8fd0\u884c(dry run)\u6765\u6d4b\u8bd5\u6d41\u7a0b,\u5728\u6bcf\u6b21\u8dd1\u6d41\u7a0b\u524d\uff0c\u90fd\u5efa\u8bae\u5148\u6267\u884cdry-run\u6765\u6392\u67e5\u6d41\u7a0b\u53ef\u80fd\u5b58\u5728\u7684\u95ee\u9898\u3002\u786e\u8ba4\u65e0\u8bef\u540e\u5728\u6700\u540e\u6267\u884c\u4efb\u52a1\u3002<\/p>\n

    $ snakemake –cores 1 -np merge.txt<\/p>\n

    <\/p>\n

    \u6700\u540e\u8f93\u5165\u76ee\u6807\u6587\u4ef6,snakemake\u4f1a\u81ea\u52a8\u6839\u636e\u8fd9\u4e9b\u6587\u4ef6\u4e32\u8d77\u6574\u4e2a\u6d41\u7a0b\u3002<\/p>\n

    \u6211\u4eec\u4e86\u89e3\u5230\u6709\u5173snakemake\u6700\u57fa\u7840\u7684\u6982\u5ff5\uff0c\u4e0b\u9762\u6211\u4eec\u5c06\u505a\u4e00\u4e2a\u5b8c\u6574\u7684\u5de5\u4f5c\u6d41\u6848\u4f8b\uff0c\u6765\u81easnakemake\u7684\u5b98\u65b9\u5b9e\u4f8b\u3002<\/p>\n

    \u7b2c\u4e8c\u4e2a\u6848\u4f8b\uff1a\u6d4b\u5e8f\u6587\u4ef6\u548c\u53c2\u8003\u57fa\u56e0\u6bd4\u5bf9\uff0c\u4e0e\u5dee\u5f02\u5206\u6790<\/h2>\n

    1.\u73af\u5883\u51c6\u5907<\/h3>\n

    $ <\/strong>mkdir snakemake-tutorial #\u521b\u5efa\u4e00\u4e2a\u5b9e\u4f8b\u76ee\u5f55<\/p>\n

    $ <\/strong>cd snakemake-tutorial<\/p>\n

    $ <\/strong>curl -L https:\/\/api.github.com\/repos\/snakemake\/snakemake-tutorial-data\/tarball -o snakemake-tutorial-data.tar.gz #\u4e0b\u8f7d\u6765\u81ea\u5b98\u7f51\u7684\u5b9e\u4f8b\u6570\u636e<\/p>\n

    $ <\/strong>tar –wildcards -xf snakemake-tutorial-data.tar.gz –strip 1 “*\/data” “*\/environment.yaml” #\u89e3\u538b\u7f29<\/p>\n

    \u4e0b\u8f7d\u7684\u6570\u636e\u5305\u62ec\u8fd9\u4e9b\u6587\u4ef6<\/strong><\/p>\n

    <\/p>\n

    $ <\/strong>mamba env create –name snakemake-tutorial –file environment.yaml #\u521b\u5efa\u865a\u62df\u73af\u5883\u547d\u540d\u4e3asnakemake-tutorial, \u5e76\u5b89\u88c5\u4f9d\u8d56environment.yaml<\/p>\n

    $ <\/strong>conda activate snakemake-tutorial #\u6fc0\u6d3b\u73af\u5883<\/p>\n

    \u6253\u5f00snakemake\u5e2e\u52a9\u6587\u6863\u770b\u4e00\u4e0b\uff0c\u5982\u679c\u80fd\u8fd4\u56de\u7ed3\u679c\uff0c\u8bf4\u660e\u5b89\u88c5\u6210\u529f\u4e86<\/p>\n

    $ <\/strong>snakemake –help<\/p>\n

    \u521b\u5efa\u4e00\u4e2aSnakefile\u6587\u4ef6<\/strong><\/p>\n

    $ vim Snakefile<\/strong><\/p>\n

    2.\u521b\u5efa\u6bd4\u5bf9\u89c4\u5219<\/h3>\n

    rule bwa_map:<\/p>\n

    input:<\/p>\n

    “data\/genome.fa”,<\/p>\n

    “data\/samples\/{sample}<\/em>.fastq”<\/p>\n

    output:<\/p>\n

    “mapped_reads\/{sample}<\/em>.bam”<\/p>\n

    shell:<\/p>\n

    “bwa mem {input}<\/em> | samtools view -Sb – > {output}<\/em>”<\/p>\n

    \u6211\u4eec\u4f7f\u7528{sample}\u901a\u914d\u7b26\uff0c\u6765\u5339\u914d\u6240\u6709\u6211\u4eec\u9700\u8981\u5904\u7406\u7684\u6587\u4ef6\u3002A\uff0cB\uff0cC.fastq<\/p>\n

    snakemake -np mapped_reads\/{A,B}.bam<\/p>\n

    \u8fd0\u884c\u7a7a\u547d\u4ee4<\/p>\n

    <\/p>\n

    \u7ed3\u679c\u6ca1\u95ee\u9898 \uff0c\u6211\u4eec\u518d\u7ee7\u7eed\u7f16\u5199\u6211\u4eec\u7684\u5de5\u4f5c\u6d41\u7a0b\u3002<\/p>\n

    3.\u5e94\u7528samtools\u5bf9bam\u6587\u4ef6\u6392\u5e8f<\/h3>\n

    rule samtools_sort:<\/p>\n

    input:<\/p>\n

    “mapped_reads\/{sample}<\/em>.bam”<\/p>\n

    output:<\/p>\n

    “sorted_reads\/{sample}<\/em>.bam”<\/p>\n

    shell:<\/p>\n

    “samtools sort -T sorted_reads\/{wildcards.sample}<\/em> ”<\/p>\n

    “-O bam {input}<\/em> > {output}<\/em>”<\/p>\n

    \u6b64\u89c4\u5219\u5c06\u4ecemapped_reads\u76ee\u5f55\u4e2d\u83b7\u53d6\u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5c06\u6392\u5e8f\u540e\u7684\u7248\u672c\u5b58\u50a8\u5728sorted_reads\u76ee\u5f55\u4e2d\u3002\u4f7f\u7528{wildcards.sample}\u6765\u901a\u914d\u8bfb\u53d6\u6587\u4ef6\u540d<\/em><\/p>\n

    4.\u5efa\u7acb\u7d22\u5f15<\/h3>\n

    rule samtools_index:<\/p>\n

    input:<\/p>\n

    “sorted_reads\/{sample}<\/em>.bam”<\/p>\n

    output:<\/p>\n

    “sorted_reads\/{sample}<\/em>.bam.bai”<\/p>\n

    shell:<\/p>\n

    “samtools index {input}<\/em>”<\/p>\n

    \u6211\u4eec\u5df2\u7ecf\u5b9a\u4e49\u4e86\u4e09\u4e2arule\uff0c\u53ef\u4ee5\u5bfc\u51fa\u62d3\u6251\u6d41\u7a0b\u56fe\u770b\u4e00\u4e0b\u3002<\/p>\n

    snakemake –dag sorted_reads\/{A,B}.bam.bai | dot -Tsvg > dag.svg<\/p>\n

    \"dag\"<\/p>\n

    5.\u751f\u6210\u57fa\u56e0\u7ec4\u53d8\u4f53<\/h3>\n

    \u8fd9\u91cc\u5e94\u7528\u4e86\u4e0a\u4e2a\u6848\u4f8b\u7684expand\u51fd\u6570<\/p>\n

    SAMPLES = [“A”, “B”]<\/p>\n

    rule bcftools_call:<\/p>\n

    input:<\/p>\n

    fa=”data\/genome.fa”,<\/p>\n

    bam=expand(“sorted_reads\/{sample}<\/em>.bam”, sample=SAMPLES),<\/p>\n

    bai=expand(“sorted_reads\/{sample}<\/em>.bam.bai”, sample=SAMPLES)<\/p>\n

    output:<\/p>\n

    “calls\/all.vcf”<\/p>\n

    shell:<\/p>\n

    “bcftools mpileup -f {input.fa}<\/em> {input.bam}<\/em> | ”<\/p>\n

    “bcftools call -mv – > {output}<\/em>”<\/p>\n

    \u8fd9\u65f6\u6211\u4eec\u518d\u753b\u4e00\u4e2a\u56fe<\/p>\n

    snakemake –dag calls\/all.vcf | dot -Tsvg > dag1.svg<\/p>\n

    \"dag1\"<\/p>\n

    6.\u4f7f\u7528\u81ea\u5df1\u7f16\u5199\u7684python\u811a\u672c<\/h3>\n

    mkdir scripts<\/p>\n

    cd scripts<\/p>\n

    vim plot-quals.py<\/p>\n

    \u4f7f\u7528\u4ee5\u4e0bpython\u811a\u672c<\/p>\n

    import<\/strong> matplotlib<\/strong><\/p>\n

    matplotlib.use(“Agg”)<\/p>\n

    import<\/strong> matplotlib.pyplot<\/strong> as<\/strong> pltfrom<\/strong> pysam<\/strong> import<\/strong> VariantFile<\/p>\n

    quals = [record.qual for<\/strong> record in<\/strong> VariantFile(snakemake.input[0])]plt.hist(quals)<\/p>\n

    plt.savefig(snakemake.output[0])<\/p>\n

    snakemake\u540c\u6837\u4e5f\u652f\u6301R\u8bed\u8a00\u811a\u672c<\/p>\n

    7.\u6dfb\u52a0snakemake\u6d41\u7a0b\u76ee\u6807\u6587\u4ef6<\/h3>\n

    rule all:<\/p>\n

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