awk for simple text manipulation

let's say you have a bed file (tab delimited):


tommy@tommy-ThinkPad-T420:~$ cat file.bed 
chr1     100 302
chr2     600 901
chr3     250 383

you want to calculate the average peak length of this file:


tommy@tommy-ThinkPad-T420:~$ cat file.bed | awk '{print $3-$2}'| awk '{sum+=$0} END {print "Average= " sum/NR}'
Average= 212

if you calculate the middle point of the peak,  $2+ ($3- $2)/2   and you get a float, you want to round the column:

cat file.bed | awk '{print $2+($3-$2)/2}'

201

750.5

316.5

tommy@tommy-ThinkPad-T420:~$ cat file.bed | awk '{print $2+($3-$2)/2}'| awk 'function round (A) { return int(A+0.5)} { printf("%d\n", round($0))}'

201

751

317

if you want to add an artificial column with peak1, peak2, peak3.....

cat file.bed | awk '{print $1"\t"$2"\t"$3"\t""peak"NR}'

chr1  100   302 peak1

chr2         600   901 peak2

chr3   250   383 peak3

if you want to change a space delimited file to a tab delimited file

cat foo.txt | awk ' -F'' { print $1"\t"$2"\t"$3 } > newfile.txt

you have two files, you want to subtract the third column of file1 (total 3 columns) from the second column of file2(total 3 columns)

paste foo1.txt  foo2.txt | awk ' { print $3 -$5}'

you want to cut column 3 from file2, cut column 1 from file 1 and put them together:

paste <(cut -f3 foo2.txt)  <(cut -f1 foo1.txt)