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awk command in shell script

I have an awk command which runs well on terminal: this awk command creates diffrent file according to their column header. awk command:

for((i=2;i<5;i++)); do awk -v i=$i 'BEGIN{OFS=FS="\t"}NR==1{n=$i}{print $1,$i > n".txt"}' ${Batch}.result.txt; done

the same command when incorporated in a shell script shows error:

Syntax error: Bad for loop variable
awk shell linux
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by mittu1602 mittu1602

Are you sure that you are executing your script with bash and not sh or dash? The latter don't like some of the bash syntax.

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written by kloetzl kloetzl

please post output from echo $SHELL

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written by cpad0112 cpad0112

Since you're using my answer from your other thread, could you please go mark it as the accepted answer?

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written by 5heikki 5heikki

Hi, I have already accepted the answer. Thank you 😊

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written by mittu1602 mittu1602

Hello mittu1602!

We believe that this post does not fit the main topic of this site.

sorry, I should have flagged this before instead of answering ; this post is not related to bioinformatics; It's just related to linux

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

i suppose you bash is sh:

$ sh
$ for((i=2;i<5;i++));  do echo $i ; done
sh: 1: Syntax error: Bad for loop variable

while it should be bash

$ bash
$ for((i=2;i<5;i++));  do echo $i ; done
2
3
4

add a shebang at the start of your script and make it executable with chmod +x

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Alternatively 

for i in $(seq 2 4); do ..; done

or

for i in 2 3 4; do ..; done

OP is probably using Ubuntu so his sh points to dash instead of bash

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written by 5heikki 5heikki

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