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.

Answer 2

Solution in perl:

#!/usr/bin/perl 

use strict; 
use warnings; 

use Data::Dumper;

my $row;

#   Open file to read.
open (my $FH, '<', 'test') or die ($!);

# Write new updated file.
open (my $OUT, '>', 'updated_test') or die ($!);


while (my $line = <$FH>){
    chomp($line);
    my @val = split( "\t" , $line );

    if ( $val[0] !~  m/rs/ ) { 
        my $row = "rs" . $val[0] . $val[1] . $val[2] . "\t" . $val[1] . "\t" . $val[2];
        print $OUT $row."\n";
    } 
    else{
        print $OUT $line."\n";
    }
}

close $FH;  
close $OUT; 

OUTPUT:

Name  Chrom  Position   
rs1     1     1234  
rs2     1     1789   
rs3     1     1289   
rs11269 1     1269   
rs11897 1     1897