bioinformatics - 执行检查点中间命令

Question

我目前遇到了一些关于 snakemake 运行检查点所需的中间规则的问题。在尝试解决此问题后，我认为问题出在 aggregate_input 函数中的 expand 命令中，但无法弄清楚为什么会这样。

这是我根据 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#data-dependent-conditional-execution 建模的来自 snakemake 的当前检查点文档

rule all:
    input:
    ¦   expand("string_tie_assembly/{sample}.gtf", sample=sample),
    ¦   expand("combined_fasta/{sample}.fa", sample=sample),
    ¦   "aggregated_fasta/all_fastas_combined.fa"




checkpoint clustering:
    input:
    ¦   "string_tie_assembly_merged/merged_{sample}.gtf"
    output:
    ¦   clusters = directory("split_gtf_file/{sample}")
    shell:
    ¦   """
    ¦   mkdir -p split_gtf_file/{wildcards.sample} ;

collapse_gtf_file.py -gtf {input} -o split_gtf_file/{wildcards.sample}/{wildcards.sample}
    ¦   """

rule gtf_to_fasta:
    input:
    ¦   "split_gtf_file/{sample}/{sample}_{i}.gtf"
    output:
    ¦   "lncRNA_fasta/{sample}/canidate_{sample}_{i}.fa"
    shell:
    ¦   "gffread -w {output} -g {reference} {input}"

rule rename_fasta_files:
    input:
    ¦   "lncRNA_fasta/{sample}/canidate_{sample}_{i}.fa"
    output:
    ¦   "lncRNA_fasta_renamed/{sample}/{sample}_{i}.fa"
    shell:
    ¦   "seqtk rename {input} {wildcards.sample}_{i} > {output}"

#Gather N number of output files from the GTF split
def aggregate_input(wildcards):
    checkpoint_output = checkpoints.clustering.get(**wildcards).output[0]
    x = expand("lncRNA_fasta_renamed/{sample}/{sample}_{i}.fa",
    ¦   sample=sample,
    ¦   i=glob_wildcards(os.path.join(checkpoint_output, "{i}.fa")).i)
    print(x)
    return x

#Aggregate fasta from split GTF files together
rule combine_fasta_file:
    input:
    ¦   aggregate_input
    output:
    ¦   "combined_fasta/{sample}.fa"
    shell:
        "cat {input} > {output}"


    ¦   aggregate_input
    output:
    ¦   "combined_fasta/{sample}.fa"
    shell:
    ¦   "cat {input} > {output}"

#Aggegate aggregated fasta files
def gather_files(wildcards):
    files = expand("combined_fasta/{sample}.fa", sample=sample)
    return(files)

rule aggregate_fasta_files:
    input:
    ¦   gather_files
    output:
    ¦  "aggregated_fasta/all_fastas_combined.fa"
    shell:
    ¦   "cat {input} > {output}"

我一直遇到的问题是，在运行这个 snakemake 文件时，combine_fasta_file 规则不会运行。花了更多时间解决这个错误后，我意识到问题是 aggregate_input 函数没有扩展，并返回一个空列表 [] 而不是我期望的列表目录中所有文件的扩展，即:lncRNA_fasta_renamed/{sample}/{sample}_{i}.fa。

这很奇怪，尤其是考虑到 checkpoint clustering 确实运行正常，并且下游输出文件在 rule all

中

有人知道为什么会这样吗？或者可能是这种情况的原因。

用于运行 snakemake 的命令:snakemake -rs Assemble_regions.snake --configfile snake_config_files/annotated_group_config.yaml

Answer 1

刚刚弄明白了。问题是我的 aggregate 命令针对错误的文件。以前我把它写成

def aggregate_input(wildcards):
    checkpoint_output = checkpoints.clustering.get(**wildcards).output[0]
    x = expand("lncRNA_fasta_renamed/{sample}/{sample}_{i}.fa",
    ¦   sample=sample,
    ¦   i=glob_wildcards(os.path.join(checkpoint_output, "{i}.fa")).i)
    print(x)
    return x

然而，这个问题是针对错误的文件。而不是 globbig {i}.fa，它应该是从 checkpoint clustering 生成的文件。所以将此代码更改为

def aggregate_input(wildcards):
    checkpoint_output = checkpoints.clustering.get(**wildcards).output[0]
    print(checkpoint_output)
    x = expand("lncRNA_fasta_renamed/{sample}/{sample}_{i}.fa",
    ¦   sample=wildcards.sample,
    ¦   i=glob_wildcards(os.path.join(checkpoint_output, "{sample}_{i}.gtf")).i)
    print(x)
    return x

解决了这个问题。