awk help for printing from a particular column till the end

Question

I have a file like this

gene    -   chr7    55675   55676   100 100
gene    -   chr7    55678   55679   100 100
gene    -   chr7    55683   55686   NP  100

The file is tab separated.

I want to change the file such that column 5 should be at column 4 and column 4 at column 5 and after that print all the columns as it is. I am showing you only 2 columns after 5th column, but there can be many more.

I tried cut -f 1,2,3,5,4,6- but it does not work.

I would prefer an awk solution for it.

Thanks

Answer 1

To swap fields 4 and 5:

$ awk -F'\t' '{a=$4; $4=$5; $5=a;} 1' OFS='\t' file
gene    -       chr7    55676   55675   100     100
gene    -       chr7    55679   55678   100     100
gene    -       chr7    55686   55683   NP      100

How it works:

• -F'\t'

  This sets the field separator on input to a tab.

• a=$4; $4=$5; $5=a

  This swaps the fourth and fifth fields.

• 1

  This is awk's cryptic shorthand for print-the-line.

• OFS='\t'

  This tells awk to use a tab as the field separator on output.

Leaving the header unchanged

To swap the fields on all lines except the first:

awk -F'\t' -v OFS='\t' 'NR>1{a=$4; $4=$5; $5=a;} 1' file

NR is the line number. The NR>1 placed before the swap commands is a condition. The swap commands will be performed only if the condition is true.

Alternate style

Some stylists recommend that the assignment to OFS be before the code:

awk -F'\t' -v OFS='\t' '{a=$4; $4=$5; $5=a;} 1' file