bash- replace empty field with . in piped statement - bash

Question

I'm looping over a list of files, while for each file im scanning for specific things to grep out.
# create .fus file
grep DIF $file | awk '{
if ( $7 != $13 )
print $4, "\t", $5, "\t", $20, "\t", $10, "\t", $11, "\t", $22, "\t", "Null";
}' > $file_name.fus
# create .inv_fus file
grep DIF $file | awk '{
if ( $7 == $13 )
print $4, "\t", $5, "\t", $20, "\t", $10, "\t", $11, "\t", $22, "\t", "Null";
}' > $file_name.inv_fus
# create .del file
echo -e '1\t1\t1\t1' > ${file_name}.del
echo -e '1\t1\t1\t3' >> ${file_name}.del
grep DEL ${file} | awk '{print $4, "\t", $5, "\t", $12, "\t", "2"}' >> ${file_name}.del
The first awk checks if the values of column 7 and 13 are different, if they are, write to file.
The second awk checks if hte values are the same, if they are, write to file. The third creates a file with 2 lines always the same, and the rest filled in by lines containing 'DEL'.
The output files I use to generate a plot, but this fails because some fields are empty. How can I change my code (I guess the awk statement ?) so that it checks for empty fields (for columns 4, 5, 20, 10, 11 and 22) and replace empty columns with dots '.' ?

Answer 1

Like the other response has said, there's a lot of simplification that could happen here, but without knowing input or expected output its hard to comment on what changes would be beneficial.
Regardless, the question seems to boil down to replacing empty fields with dots in your output for some process down the line. Adding a function like this to your awk scripts would seem to do the trick:
function clean() {
for(i = 1; i <= NF; i++) { if($i==""){$i="."}; }
}
For example, given this input in test.txt:
a1,a2,a3,a4
b1,,b3,b4
,,c3,
d1,d2,d3,
Running the following awk results in empty fields being periods.
awk -F',' 'function clean() {
for(i = 1; i <= NF; i++) { if($i==""){$i="."}; }
}
BEGIN {OFS=","}
{clean(); print;}' test.txt
Example output:
a1,a2,a3,a4
b1,.,b3,b4
.,.,c3,.
d1,d2,d3,.

Answer 2

Let's start by cleaning up your script. Replace the whole thing with just one simple awk command:
awk -v file_name="$file_name" '
BEGIN {OFS="\t"; print 1, 1, 1, 1 ORS 1, 1, 1, 3 > (file_name ".del")}
/DIF/ {print $4, $5, $20, $10, $11, $22, "Null" > (file_name "." ($7==$13?"inv_":"") "fus")}
/DEL/ {print $4, $5, $12, 2 > (file_name ".del")}
' "$file"
Now, update your question with sample input and expected output that captures what else you need it to do.