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=; my @arr2=; 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++; } } }