Snakemake. Problem with awk

Question

[kamanovae]

Hi!

I have a problem with the awk that looks like this:

awk: cmd. line:1: {if(NR%4==1) {printf("">%s
awk: cmd. line:1:                         ^ syntax error
[Wed Jun 30 16:46:02 2021]
Error in rule univec:
    jobid: 0
    output: out_univec/SRR13510812_1.fasta, out_univec/SRR13510812_2.fasta

RuleException:
CalledProcessError in line 63 of /storage1/kaman/Ldec_all/snakefile:
Command 'set -euo pipefail;  cat out/SRR13510812_1_nohg38.fastq | awk '{if(NR%4==1) {printf("">%s

my code looks like this. I guess I somehow need to screen part of awk command

rule univec:
        input: data1=config["out"] + "{sample}_1_nohg38.fastq", data2=config["out"] + "{sample}_2_nohg38.fastq"
        output: output1=config["out_univec"] + "{sample}_1.fasta", output2=config["out_univec"] + "{sample}_2.fasta"
        run:
                shell("""cat {input.data1} | awk '{{if(NR%4==1) {{printf("">%s\n"",substr($0,2));}} else if(NR%4==2) print;}}' > {output.output1}""")
                shell("""cat {input.data2} | awk '{{if(NR%4==1) {{printf("">%s\n"",substr($0,2));}} else if(NR%4==2) print;}}' > {output.output2}""")

Thanks!

[Pierre Lindenbaum]

how about using a """ section ?

 shell: """
         awk '{{if(NR%4==1) {{printf(">%s\n",substr($0,2));}} else if(NR%4==2) print;}}'  {input.data1}  > {output.output1}
        """

[kamanovae]

it doesn't help either. This error appears:

awk: cmd. line:1: {if(NR%4==1) {printf(">%s
awk: cmd. line:1:                      ^ unterminated string
awk: cmd. line:1: {if(NR%4==1) {printf(">%s
awk: cmd. line:1:                      ^ syntax error
[Wed Jun 30 17:05:11 2021]
Error in rule univec:
    jobid: 13
    output: out_univec/SRR13510812_1.fasta, out_univec/SRR13510812_2.fasta
    shell:
         awk '{if(NR%4==1) {printf(">%s
",substr($0,2));} else if(NR%4==2) print;}'  out/SRR13510812_1_nohg38.fastq  > out_univec/SRR13510812_1.fasta
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Answer 1

[Pierre Lindenbaum]

ah ! I think you need to escape the \n to \\n

[kamanovae]

Thanks! It really works!

[ATpoint]

Could you post the final working command so others may benefit from it?

[kamanovae]

It's my final code:

   rule univec:
            input: data1=config["out"] + "{sample}_1_nohg38.fastq", data2=config["out"] + "{sample}_2_nohg38.fastq"
            output: output1=config["out_univec"] + "{sample}_1.fasta", output2=config["out_univec"] + "{sample}_2.fasta"
            run:
                    shell(""" awk '{{if(NR%4==1) {{printf(">%s\\n",substr($0,2));}} else if(NR%4==2) print;}}'  {input.data1}  > {output.output1}""")
                    shell(""" awk '{{if(NR%4==1) {{printf(">%s\\n",substr($0,2));}} else if(NR%4==2) print;}}'  {input.data2}  > {output.output2}""")