#!/usr/bin/perl use warnings; use strict; my (%Chr, %R); my (@key_split, @reg_split); my ($reg_line); open(KEY, ") { chomp; @key_split = split("\n"); $Chr{"$key_split[0]"} = $key_split[0]; } while () { chomp; @reg_split = split("\t"); #$R{"$reg_split[0]"} = ($reg_split[0], $reg_split[1], $reg_split[2], $reg_split[3]); $R{"$reg_split[0]"} = $reg_split[0]; } foreach my $key (keys %Chr) { if(exists($R{$key})){ print ("$R{$key}\n"); } } close(KEY); close(REG);