Question

I am extracting characters from string at certain positions with this command:

left=1; right=4; grep ETM21CH01EPU3Z -A1 SLf_454.fna | tail -n 1 | awk '{print substr($0,1,4)}'

and getting this correct output:

GTTG

Now I would like to replace 1 and 4 by values in bash variables left and right.

I tried this:

left=1; right=4; grep ETM21CH01EPU3Z -A1 SLf_454.fna | tail -n 1 | awk -v l=$left r=$right '{print substr($0,l,r)}'

awk: cmd. line:1: fatal: cannot open file `{print substr($0,l,r)}’ for reading

Any suggestions, please? Thanks.

EDIT: copied from comment below so we can actually read it:

Well, I also have a file, where is written what to search (for example ETM21CH01EPU3Z) and at which positions. So the whole code is:

while read -r line; do
   echo $line;
   name=`echo $line | cut -d' ' -f 1`;
   left=`echo $line | cut -d' ' -f 2`;
   right=`echo $line | cut -d' ' -f 3`;
   grep $name -A1 SLf_454.fna | tail -n 1 | awk -v l=$left -v r=$right '{print substr($0,l,r)}';
done < CL6o_blastoutput_SLf_454.fna_out 

Answer 1

You’re missing a -v before your right variable. Every variable that you want to pass into awk must be preceded by a -v.

Change it to:

awk -v l=$left -v r=$right '{print substr($0,l,r)}'