snakemake文件中ABRICATE csv结果的连接

问题描述 投票:0回答:1

我想将程序ABRICATE(github.com/tseemann/abricate)的多个csv文件结果串联到单个csv文件中。

以下snakefile通过fasta文件的文件夹运行,从而为每个fasta生成一个单独的csv。我想将这些结果串联到单个csv文件中,但不确定如何构建“全部规则”。

有什么建议吗?下面是我的工作蛇文件。谢谢

########################### snakefile making dictionary
import os
import yaml

file_list = []
### location assumes that data is in results_fasta/ folder
for entry in os.scandir("results_fasta/"):
    if entry.is_file():
        file_list.append(entry.name)

#### this tells split the file for use in dictionary creation
config_dict = {"samples":{i.split(".")[0]:"results_fasta/"+i for i in file_list}}

with open("config_abricate_resfinder.yaml","w") as handle:
    yaml.dump(config_dict,handle)

###### dictionary created using all files located in results_fasta folder
configfile: "config_abricate_resfinder.yaml"

##### not needed but used to say what is currently running
print("Starting abricate workflow")

##### rule all is a general rule that says this is the results we are lookin for in the end.
rule all:
    input:
        expand("abricate_resfinder/{sample}_abricate_resfinder.csv", sample = config["samples"])

##### Abricate resfinder
rule resfinder:
    input:
        lambda wildcards: config["samples"][wildcards.sample]
    params:
        db_resfinder = "leaveblank",  ### for resfinder DB is default so leave blank
        type = "csv"
    output:
        res = "abricate_resfinder/{sample}_abricate_resfinder.csv",
######## log file is empty.  need to print stdout to log
    log:
        "logs/{sample}_resfinder.log"
    shell:
        "abricate {input} --{params.type} > {output.res}"
python csv snakemake
1个回答
0
投票

如果文件没有标题并且字段匹配,则可以通过cat命令进行串联:

rule all:
    input:
        expand("abricate_resfinder/{sample}_abricate_resfinder.csv", sample = config["samples"])
    output:
        out.csv
    shell:
        "cat {input} > {output}"

如果有标题,则需要首先考虑实际需要的结果。最简单的方法是完全删除所有标头。您可以尝试以下方法:

    "cat {input} | sed '/^#/d' > {output}"
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