Hello All, I am very new to perl, and I have two files tab separated: File1:

   rs492602    **CC**     Vitamin B12 deficiency    FUT2    Higher lev
+els of vitamin B12        
        rs492602    CT    Vitamin B12 deficiency    FUT2    Normal lev
+els of vitamin B12        
        rs492602    TT     Vitamin B12 deficiency    FUT2    Normal le
+vels of vitamin B12
[download]

File2:

        rs492602    **GG**    exm-rs492602
        rs492602    **CC**    exm-rs492602
[download]

Result:

rs492602**CC** **GG** Vitamin B12 deficiency    FUT2    Higher levels 
+of vitamin B12    
    rs492602**CC** **CC** Vitamin B12 deficiency    FUT2    Higher lev
+els of vitamin B12
[download]

So far I have tried this which matches only the RS_ids and not the basepairs:

use warnings;
use strict;

open(F1,$ARGV[0]) or die("could not open $ARGV[0] due to $!\n");
open(F2,$ARGV[1]) or die("could not open $ARGV[1] due to $!\n");

my @arr1=<F1>;
my @arr2=<F2>;
chomp(@arr1);
chomp(@arr2);

my $x=shift(@arr1);
my $i=0;

print "$x\n";

foreach my $line1(@arr2){
    chomp($line1);
    foreach my $line2(@arr1){
        chomp($line2);
        $line2=~/(\w+)\t.*/;
        my $rsid=$1;
        #while($rsid){
        #    $i++;
        #}
        if($line1 eq $rsid){
            print "$line2\n";
            $i++;
        }
        
    }
}
[download]

Thank you!

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