I'm facing an error while converting my bash comand to shell script syntax error in shell scrip-CodePudding

#!/bin/bash

set -o errexit
set -o nounset

#VAF_and_IGV_TAG

paste <(grep -v "^#" output/"$1"/"$1"_Variant_Filtering/"$1"_GATK_filtered.vcf | cut -f-5) \
      <(grep -v "^#" output/"$1"/"$1"_Variant_Filtering/"$1"_GATK_filtered.vcf | cut -f10-| cut -d ":" -f2,3) |
sed 's/:/\t/g' |
sed '1i chr\tstart\tend\tref\talt\tNormal_DP_VCF\tTumor_DP_VCF\tDP'|
awk 'BEGIN{FS=OFS="\t"}{sub(/,/,"\t",$6);print}' \
  > output/"$1"/"$1"_Variant_Annotation/"$1"_VAF.tsv

My above code ends up with a syntax error if I run this in the terminal without using the variable it shows no syntax error

sh Test.sh S1 Test.sh: 6: Test.sh: Syntax error: "(" unexpected

paste <(grep -v "^#" output/S1/S1_Variant_Filtering/S1_GATK_filtered.vcf | cut -f-5) \
      <(grep -v "^#" output/S1/S1_Variant_Filtering/S1_GATK_filtered.vcf | cut -f10-| cut -d ":" -f2,3) |
sed 's/:/\t/g' |
sed '1i chr\tstart\tend\tref\talt\tNormal_DP_VCF\tTumor_DP_VCF\tDP'|
awk 'BEGIN{FS=OFS="\t"}{sub(/,/,"\t",$6);print}' \
  > output/S1/S1_Variant_Annotation/S1_VAF.ts

My vcf file looks like this: https://drive.google.com/file/d/1HaGx1-3o1VLCrL8fV0swqZTviWpBTGds/view?usp=sharing

CodePudding user response：

You cannot use <(command) process substitution if you are trying to run this code under sh. Unfortunately, there is no elegant way to avoid a temporary file (or something even more horrid) but your paste command - and indeed the entire pipeline - seems to be reasonably easy to refactor into an Awk script instead.

#!/bin/sh

set -eu

awk -F '\t' 'BEGIN { OFS=FS;
        print "chr\tstart\tend\tref\talt\tNormal_DP_VCF\tTumor_DP_VCF\tDP' }
    !/#/ { p=$0; sub(/^([^\t]*\t){9}/, "", p);
           sub(/^[:]*:/, "", p); sub(/:.*/, "", p);
           sub(/,/, "\t", p);
           s = sprintf("%s\t%s\t%s\t%s\t%s\t%s", $1, $2, $3, $4, $5, p);
           gsub(/:/, "\t", s);
           print s
    }' output/"$1"/"$1"_Variant_Filtering/"$1"_GATK_filtered.vcf \
  > output/"$1"/"$1"_Variant_Annotation/"$1"_VAF.tsv

Without access to the VCF file, I have been unable to test this, but at the very least it should suggest a general direction for how to proceed.

CodePudding user response：

sh, does not support bash process substitution <(). The easiest way to port it is to write out two temporary files, and remove them via when via a trap when done. The better option is use a tool that is sufficiently powerful (i.e. sed) to do the filtering and manipulation required:

#!/bin/sh
header="chr\tstart\tend\tref\talt\tNormal_DP_VCF\tTumor_DP_VCF\tDP"
field_1_to_5='\(\([^\t]*\t\)\{5\}\)' # \1 to \2
field_6_to_8='\([^\t]*\t\)\{4\}[^:]*:\([^,]*\),\([^:]*\):\([^:]*\).*' # \3 to \6
src="output/${1}/${1}_Variant_Filtering/${1}_GATK_filtered.vcf"
dst="output/${1}/${1}_Variant_Variant_Annotation/${1}_VAF.tsv"
sed -n \
  -e '1i '"$header" \
  -e '/^#/!s/'"${field_1_to_5}${field_6_to_8}"'/\1\4\t\5\t\6/p' \
  "$src" > "$dst"

If you are using awk (or perl, python etc) just port the script to that language instead.

As an aside, all those repeated $1 suggest you should rework your file naming standard.