manipulating a shell script

Question

I have a shell script which does couple of things like storing values in a variable. As an example here is my script:

for i in ../../*.bam do fn=$(basename $i) fn=${fn%_Aligned.sortedByCoord.out.bam} bamToBed -i $i | awk -v OFS="\t" '{if($6 ~ /+/){print $1,$2+67,$2+67+1,$4,$5,$6}else{print $1,$3-67-1,$3-67,$4,$5,$6}}' | awk -v OFS="\t" '$3 > 0' > ${fn}_pos.bed sortBed -g $genome -i ${fn}_pos.bed > ${fn}_n_pos.bed mv ${fn}_n_pos.bed ${fn}_pos.bed perl counter.pl ${fn}_pos.bed | sortBed -g $genome -i stdin | intersectBed -g $genome -sorted -a <(cat $genome | awk -v OFS="\t" '{print $1,"0",$2}') -b stdin -wa -wb | cut -f 4-7 > ${fn}.bedGraph bedGraphToBigWig ${fn}.bedGraph $genome ${fn}.bw a=`samtools view $i | wc -l` intersectBed -g $genome -sorted -c -a <(cat test.bed | awk -v OFS="\t" '{print $1,$2-50,$2+400,$4,$5,$6}') -b ${fn}_pos.bed | cut -f 4,7 | awk -v OFS="\t" '{print $1,$2,$a}'> ${fn}_IP_count.txt cat ${fn}_IP_count.txt | awk -v OFS="\t" '{print $1,$2,$a}' > final.txt done 

As you can see this line in the code where I have declared a variable a. This stores a number. Then I created a 2 column text file, tab delimited ${fn}_IP_count.txt I want to add a third column in this file where the third column is the value stored in the variable a to every line. As an example,2 column file looks like this:

gene1 200 gene2 23 gene3 45 gene4 10 

Let's say the value stored in the variable a is 245676, then I want the output to be stored in the third column like this

gene1 200 245676 gene2 23 245676 gene3 45 245676 gene4 10 245676 

I tried it using awk but I am not getting the right answer. Any help would be appreciated.

Answer 1

You pass other variables in the same way as you are passing OFS, using -v

Ex.

awk -v OFS="\t" -v a="$a" '{print $1,$2,a}'