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.