如何在Snakemake中进行部分扩展? [英] How to do a partial expand in Snakemake?

问题描述

我尝试先为LETTERS x NUMS组合生成4个文件，然后对NUMS进行汇总，以在LETTERS中为每个元素获取一个文件:

I'm trying to first generate 4 files, for the LETTERS x NUMS combinations, then summarize over the NUMS to obtain one file per element in LETTERS:

LETTERS = ["A", "B"]
NUMS = ["1", "2"]


rule all:
    input:
        expand("combined_{letter}.txt", letter=LETTERS)

rule generate_text:
    output:
        "text_{letter}_{num}.txt"
    shell:
        """
        echo "test" > {output}
        """

rule combine text:
    input:
        expand("text_{letter}_{num}.txt", num=NUMS)
    output:
        "combined_{letter}.txt"
    shell:
        """
        cat {input} > {output}
        """

执行此蛇文件会导致以下错误:

Executing this snakefile results in the following error:

WildcardError in line 19 of /tmp/Snakefile:
No values given for wildcard 'letter'.
  File "/tmp/Snakefile", line 19, in <module>

似乎不可能部分expand.是expand的限制吗?如果是这样，我应该如何规避呢?

It seems that partial expand is not possible. Is it a limitation of expand ? If so, how should I circumvent it ?

推荐答案

似乎这不是expand的限制，而是我对python字符串格式工作方式的熟悉程度的限制.对于非扩展的通配符，我需要使用双括号:

It seems that this is not a limitation of expand, but a limitation of my familiarity with the way string-formatting works in python. I need to use double brackets for the non-expanded wildcard:

LETTERS = ["A", "B"]
NUMS = ["1", "2"]


rule all:
    input:
        expand("combined_{letter}.txt", letter=LETTERS)

rule generate_text:
    output:
        "text_{letter}_{num}.txt"
    shell:
        """
        echo "test" > {output}
        """

rule combine text:
    input:
        expand("text_{{letter}}_{num}.txt", num=NUMS)
    output:
        "combined_{letter}.txt"
    shell:
        """
        cat {input} > {output}
        """

现在执行此蛇文件会生成预期的以下文件:

Executing this snakefile now generates the expected following files:

text_A_2.txt
text_A_1.txt
text_B_2.txt
text_B_1.txt
combined_A.txt
combined_B.txt

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