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

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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!

#!/usr/bin/perl -w
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;
                
        }
     }
 }

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In reply to Regular expression help by ananassa

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