We use a script that prints bash commands into a file that is then run on an HPC system. It is supposed to run through a large text file containing geographic coordinates separated by whitespace and extract a specific region from that file (e.g. extract all lines with an x coordinate between xmin and xmax and an y coordinate between ymin and ymax).
Ideally, I'd like to use awk for that like so (from memory since I don't have my computer available at the moment):
awk -v xmin=-13000 -v xmax=13000 -v ymin=-500 -v ymax=500 -F ' ' {if ($1 > xmin && $1 < xmin && $2 > ymin && $2 < ymin) print $1 $2} $infile > $outfile
That would probably execute fine. However, as suggested by the title, we save this line indirectly for 25 regions, each with their own xmin, xmax etc. There are more operations following after that (using GMT calls etc). Here's a little snippet:
xmin=-13000
xmax=13000
ymin=-500
ymax=500
infile=./full_file.txt
outfile=./filtered_file.yxy
srcfile=./region_1.txt
echo """awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -F ' ' {if ($1 > $xmin && $1 < $xmin && $2 > $ymin && $2 < $ymin) print $1 $2} $infile > $outfile""" >> $srcfile
Obviously, this raises errors when running due to variable expansion. I've tried escaping the awk column identifiers but to no avail or didn't understand the pattern correctly. Could someone point me to a solution that allows us to keep the indirect approach?
IIUC, you have to either escape each dollar sign like that:
{if (\$1 > xmin && \$1 < xmin
or temporarily close a double quote and put a dollar sign in a single quote:
"{if ("'$1'" > xmin && "'$1'" < xmin"
or use Bash specific %q printf specifier:
$ read
awk -v xmin=-13000 -v xmax=13000 -v ymin=-500 -v ymax=500 -F ' ' {if ($1 > xmin && $1 < xmin && $2 > ymin && $2 < ymin) print $1 $2} $infile > $outfile
$ printf "%q\n" "$REPLY"
awk\ -v\ xmin=-13000\ -v\ xmax=13000\ -v\ ymin=-500\ -v\ ymax=500\ -F\ \'\ \'\ \{if\ \(\$1\ \>\ xmin\ \&\&\ \$1\ \<\ xmin\ \&\&\ \$2\ \>\ ymin\ \&\&\ \$2\ \<\ ymin\)\ print\ \$1\ \$2\}\ \$infile\ \>\ \$outfile
$ echo awk\ -v\ xmin=-13000\ -v\ xmax=13000\ -v\ ymin=-500\ -v\ ymax=500\ -F\ \'\ \'\ \{if\ \(\$1\ \>\ xmin\ \&\&\ \$1\ \<\ xmin\ \&\&\ \$2\ \>\ ymin\ \&\&\ \$2\ \<\ ymin\)\ print\ \$1\ \$2\}\ \$infile\ \>\ \$outfile
awk -v xmin=-13000 -v xmax=13000 -v ymin=-500 -v ymax=500 -F ' ' {if ($1 > xmin && $1 < xmin && $2 > ymin && $2 < ymin) print $1 $2} $infile > $outfile
And also I think it would be good to enclose awk code in ' if you don't want shell to expand variables.