CODEWITHSUNDEEP
bashprintingawknull
Vonton
Vonton

Reputation: 3344

Print awk for empty row

I have one problem. I am using this code in bash and awk:

#!/bin/bash
awk 'BEGIN {print "CHR\tSTART\tSTOP\tPOCET_READU\tGCcontent"}'
for z in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 

do 
export $z
for i in {0..249480000..60000}
    do
u=$i
let "u +=60000"
export $i 
export $u 

samtools view /home/filip/Desktop/AMrtin\ Hynek/highThan89MapQ.bam  chr$z:$i-$u | awk '{ n=length($10); print gsub(/[GCCgcs]/,"",$10)/n;}'| awk -v chr="chr"$z -v min=$i -v max=$u '{s+=$1}END{print chr,"\t",min,"\t",max,"\t",NR,"\t",s/NR}}'   
done 
done

From this I am getting the result like this:

chr1 60000 120000 30 0.333

chr3 540000 600000 10 0.555

The step of loop is 60000, but if I divide s/NR, sometimes the NR is 0 and this row is not in output. Thank I wan to get if the NR=0 and s/NR does not exist (because we cannot divide by 0):

chr1 0 60000 N/A N/A

chr1 60000 120000 30 0.333

chr3 480000 540000 N/A N/A

chr3 540000 600000 10 0.555

I tried use condition like

{s+=$1}END{print chr,"\t",min,"\t",max,"\t",NR,"\t",s/NR; if (S/NR == "") print chr,"\t",min,"\t",max,"\t","N/A","\t","N/A"}' But it doesnt work. Could you help me please?

Upvotes: 0

Views: 94

Answers (1)

Barmar
Barmar

Reputation: 780818

The problem is you're dividing by zero, which is an error. You need to test NR before doing the division.

awk -v chr="chr"$z -v min=$i -v max=$u '
    {s+=$1}
    END {print chr, "\t", min, "\t", max, "\t", (NR ? NR : "N/A"), "\t", (NR ? s/NR : "N/A")}'

Upvotes: 1

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