Shell Programming and Scripting

Hi friends,
I am beginner in shell scripting. I am trying to modify (Reorder and insert column) a BIG .txt file using awk to create a .bim file. My start file has 25 columns But I need to make a new file with only 5 columns from the start file and insert a new column in position 3 with value '0'.

To do this first I tried to reorder the columns and create and empty colum at 3rd column, then thought to input zero in it.
But first step didn't work

Code:

awk -F ' ' {printf "%s\t%s\t%s\t%s\t%s\t%s",$15,$2,$0,$16,$4,$5;} <test.txt> test.bim

but always getting error as

Code:

-bash: syntax error near unexpected token `}'

I tried different similar options but nothing worked.

Any help will be really great.
Thanks a lot,
Smitra

you must put the awk code between quotes !

Code:

awk -F ' ' '{printf "%s\t%s\t%s\t%s\t%s\t%s",$15,$2,$0,$16,$4,$5;}' <test.txt> test.bim

First of all, you need to quote your script to prevent processing by shell. Also, there is no need for -F' ' as the default FS (field separator) in awk is a space. Also, $0 means the whole input line and not zero. So, your line should be:

Code:

awk '{printf "%s\t%s\t%s\t%s\t%s\t%s",$15,$2,"0",$16,$4,$5;}' <test.txt> test.bim

Thanks a lot to both of you for your reply. Actually I don't have any methodical training in this so often makes silly mistakes.
Can you please tell in which cases do I need FS?
Thanks,
Mitra

When your field separator is something other than whitespace (e.g. if you were processing a simple CSV file you would use a comma instead).

thanks CarloM