CODEWITHSUNDEEP
snakemake
L-Moon
L-Moon

Reputation: 21

NameError when ues awk in snakemake

First, here is a test example (Snakefile):

rule test:
    input:"path/file1", "path/file2"
    output:"path/file3"
    shell:
        """
        awk 'NR==FNR{score[$3]=$5;next}{{sum=0}for(i=$2;i<=$3;i++){sum+=score[i]}printf "%-10s\\t%-10s\\n",sum,$4}' {input[0]} {input[1]} >> {output}
        """

When I run this script, it returns NameError: The name 'score' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}, I have tried to {score} or replicate {}, but all doesn't work. So, I want to know how to solve this quetion. Thanks.

Upvotes: 2

Views: 911

Answers (1)

Maarten-vd-Sande
Maarten-vd-Sande

Reputation: 3701

That is because snakemake tries to format the text and put the variables in the string. Since e.g. score are part of the script, snakemake can not deduce which variable it belongs to and it crashes. To escape this behaviour use double curly brackets: {{score[$3]}}. It gets rather ugly with multiple curly brackets, like in your rule

rule test:
    input:"path/file1", "path/file2"
    output:"path/file3"
    shell:
        """
        awk 'NR==FNR{{score[$3]=$5;next}}{{{{sum=0}}for(i=$2;i<=$3;i++){{sum+=score[i]}}printf "%-10s\\t%-10s\\n",sum,$4}}' {input[0]} {input[1]} >> {output}
        """

(I hope I didn't miss any, but I think you get the idea)

Upvotes: 4

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