Deal all,

I need to find match between two tab delimited files files like this:

File 1:

ID1 1 65383896 65383896 G C PCNXL3 ID1 2 56788990 55678900 T A ACT1 ID1 1 56788990 55678900 T A PRO55

File 2

ID2 34 65383896 65383896 G C MET5 ID2 2 56788990 55678900 T A ACT1 ID2 2 56788990 55678900 T A HLA

what I would like to do is to retrive the matching line between the two file. What I would like to match is everyting after the gene ID

So far I have written this code but unfortunately perl keeps giving me the error: use of "Use of uninitialized value in pattern match (m//)"

Could you please help me figure out where i am doing it wrong?

Thank you in advance!

use strict;

open (INA, $ARGV[0]) || die "cannot to open gene file";
open (INB, $ARGV[1]) || die "cannot to open coding_annotated.var files";

my @sample1 = <INA>;
my @sample2 = <INB>;


foreach my $line (@sample1) {
    my @tab = split (/\t/, $line);

my $chr = $tab[1];
my $start = $tab[2];
my $end = $tab[3];
my $ref = $tab[4];
my $alt = $tab[5];
my $name = $tab[6];
    foreach my $item (@sample2){
    my @fields = split (/\t/,$item);


        if ($fields[1]=~ m/$chr(.*)/ && $fields[2]=~ m/$start(.*)/ && $fields[4]=~ m/$ref(.*)/ && $fields[5]=~ m/$alt(.*)/&& $fields[6]=~ m/$name(.*)/){        
            print  $line,"\n",$item;
        }
    }
}