use strict; open (FILEHANDLE, "$ARGV[0]") || die("Could not open file 1 input file"); my @file1 = ; close (FILEHANDLE); open (FILE2, "$ARGV[1]") || die ("Could not open file 2 input file"); my @SAVI = ; close (FILE2); foreach my $line1 (@file1) { chomp ($line1); (my $var1, my $var2) = split(/\t/,$line1); foreach my $line2 (@file2) { chomp($line2); (my $Var1, my $Var2)= split(/\t/,$line2); if ($var1=~m/$Var1/) { print $line1 ."\t" . $line2 . "\n"; } } }