syntax error near unexpected token `(' : output awk result as variable

Asked Oct 29 '18 at 15:18

Active Oct 29 '18 at 15:18

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I want to process a tab-limited file text using awk and set the output as variable in unix.

I wanted to i) select lines that have unique combinations of values in the 1st and 3rd column; ii) sort by increasing numeric value at the first column; iii) extract the first column; etc.. So I used the following script:

locus_overmerged=$(awk -F"\t" '!seen[$1, $3]++' <(gzip -dc $id) | sort -n -k1,1 | cut -f1 | uniq -dc | awk '{print $2}')

If I run it by hand in the terminal, it works. However, when I input this command in a script, I obtain the following error:

syntax error near unexpected token `('
` awk -F"\t" '!seen[$1, $3]++' <(gzip -dc $id) | sort -n -k1,1 | cut -f1 | uniq -dc | awk '{print $2}' )'

Any idea on what it could be the problem?

asked Oct 29 '18 at 15:18

CafféSospeso

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`<(...)` is bash-only syntax; this looks like you're running your script with `/bin/sh`. Check that it's actually being run with bash -- with a `#!/bin/bash` shebang, and **not** being invoked using `sh scriptname`. – Charles Duffy Oct 29 '18 at 15:20
yes, It is a #!/bin/sh script. – CafféSospeso Oct 29 '18 at 15:21
BTW, unrelated to the syntax error, but `gzip -dc <"$id"` or `gzip -dc -- "$id"` is going to be a bit more reliable; unquoted expansions have some undesirable side effects. – Charles Duffy Oct 29 '18 at 15:22
...yup, can't use that syntax in `/bin/sh` (and questions about that language should be tagged `sh`, not `bash`). – Charles Duffy Oct 29 '18 at 15:22
Ok, you were right. I replaced /bin/sh with /bin/bash – CafféSospeso Oct 29 '18 at 15:48

syntax error near unexpected token `(' : output awk result as variable

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