Using linux to find and replace the a value in a column in a tab delimited file

Question

I have this data below for example:

Name  Chrom  Position

rs1    1     1234  

rs2    1     1789   

rs3    1     1289   

1      1     1269   

2      1     1897

I would like to find all the lines in the first column that DO NOT contain the string "rs" and replace with

rs'chrom''position'

. Name 1 would look like

rs11269

.

It would end up looking like this:

Name  Chrom  Position   

rs1     1     1234  

rs2     1     1789   

rs3     1     1289   

rs11269 1     1269   

rs11897 1     1897

I know with awk I can do

awk '!/rs/{print $1}' file

and it will find all the lines in the first column that do not contain the string "rs" but how do I take this further now to replace it with my own rs ID built from chrom and position? Would I use gsub or something else? This doesn't have to be in shell commands but also Perl is another option to use as well. Thank you for your help.

Answer 1

You can use this command:

$ awk 'BEGIN{FS=OFS="\t"}NR>1&&!($1~/rs/){$1="rs"$2$3}1' file
Name     Chrom  Position
rs1      1      1234
rs2      1      1789
rs3      1      1289
rs11269  1      1269
rs11897  1      1897

With BEGIN{FS=OFS="\t"} we set the input and output field separators to the tab character, with NR>1&&!($1~/rs/) we filter the lines that are not the first (header) and that do not contain the string "rs" in the first field, and with {$1="rs"$2$3} we change the value of the first field to the desired value. The final 1 is the true condition, so that all lines are printed.

Using linux to find and replace the a value in a column in a tab delimited file

Sign up