#!/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>;

# use map for this maybe?
foreach my $line (@sample1) {
    my ($id, $rest) = split( '\t', $line, 2);
    chomp ($rest);
    $hash1{$rest} = $id;
}

foreach my $line (@sample2) {
    my ($id, $rest) = split( '\t', $line, 2);
    chomp( $rest);
    if (exists($hash1{$rest}) {
       print "Match: $line\n";
    }
}