#!/usr/bin/perl use strict; use warnings; open(FH, "outputps_scan_chr1_.out") or die "Can't Open File1\n"; my @array1=; close(FH); open(BH, "chr1_1.txt") or die "Can't Open File2\n"; my @array2=; close(BH); my $pat='qr/^LOC_Os0.../'; foreach my $line1(@array1) { my @array3= split(/ /, $line1); foreach my $line2(@array2) { my @array4= split(/ /, $line2); foreach my $line3(@array3) { foreach my $line4(@array4) { $line3=~ $pat; $line4=~ $pat; if ($line3 eq $line4) { print $line3; } else { print "nothing to right\n"; } } } } }