escaping brackets and other characters in shell script

Question

I have run the following command on the command line and it works fine, but when I try running it from a shell script and run shell script from the terminal I get the following error:

join -t $'\t' -a1 -e "u" -1 1 -2 1 -o 1.1,2.1,2.2 file1 \ <(cat file2 | sort -k1,1|tr [:blank:] \\t ) | awk 'BEGIN {FS="\t";OFS="\t"}{if \($2 == "u")print $0, $1;else print $0, $3}' | awk '{gsub(/ /,"\t");l=$4; sub(/.*_/,"",l); print $2"\t"$3"\t"l}' > out

syntax error near unexpected token('`

I have tried escaping the bracket but it still gives me the same error. I have many of these multi-layered commands in the script so I am sure this will be a problem in other parts, is there a way to solve this?

Answer 1

What you have lost is the trailing ) on your stdin subclause. What I suspect you have gained is a headache trying to read your code.

Try this instead, which then lends itself to further optimisation because it's (more) readable:

tr '[:blank:]' $'\t' <file2 |
    awk '
        BEGIN { FS="\t"; OFS="\t" }
        { if ($2 == "u") print $0, $1; else print $0, $3 }
    ' |
    awk '
        { gsub(/ /,"\t"); l=$4; sub(/.*_/,"",l); print $2 "\t" $3 "\t" l }
    ' |
    sort |
    join -t $'\t' -a1 -e "u" -1 1 -2 1 -o 1.1,2.1,2.2 file1 - >out