awk command in shell script

Question: (Closed) awk command in shell script

11 months ago by

mittu1602 • 150

India

mittu1602 • 150 wrote:

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

linux shell awk • 816 views

ADD COMMENT • link •

modified 11 months ago by Pierre Lindenbaum ♦ 113k • written 11 months ago by mittu1602 • 150

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.

ADD REPLY • link written 11 months ago by kloetzl • 990

please post output from echo $SHELL

ADD REPLY • link written 11 months ago by cpad0112 • 9.4k

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

ADD REPLY • link written 11 months ago by 5heikki ♦ 7.8k

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

ADD REPLY • link written 11 months ago by mittu1602 • 150

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!

ADD REPLY • link written 11 months ago by Pierre Lindenbaum ♦ 113k

11 months ago by

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 113k wrote:

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

ADD COMMENT • link modified 11 months ago • written 11 months ago by Pierre Lindenbaum ♦ 113k

Alternatively

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

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

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

ADD REPLY • link modified 11 months ago • written 11 months ago by 5heikki ♦ 7.8k