Great Thanks. I had just realized the that I had to move the declaration to outside of the if else loop. I also like the idea of a subroutine. Subroutine is now working. Here working code for any following this thread

new code

############### read in blast table and parse #######
my $in_blast_tab=$ARGV[0];
open(IN,$in_blast_tab) or die "cannot open $in_blast_tab\n";

my %HoFlg1; my %HoFlg2;
#my $Flag1; my $Flag2;

while (my $line=<IN>) {
        chomp $line;
        my ($Query_id,$strand,$Subj_id,$Perc_iden,$align_len,$num_mm,$
+gap,$q_start,$q_end,$s_start,$s_end,$e_value,$bit_score)=split("\t",$
+line); # extra field of strand
        next if ($bit_score <60);
        my ($Flag1, $Flag2 ) = &Flag( $Subj_id, \%proph_prots, \%euk_p
+rots, \%vir_prots );
        $HoFlg1{$Query_id}{$Subj_id}{$bit_score}=$Flag1;
        $HoFlg2{$Query_id}{$Subj_id}{$bit_score}=$Flag2;
        print join("\t",$Query_id,$Subj_id,$bit_score,$Flag1,$Flag2)."
+\n";
}

sub Flag {
        my $Subj_id=$_[0];
        my $proph_prots=$_[1];
        my $euk_prots=$_[2];
        my $vir_prots=$_[3];
        my $Flag1; my $Flag2;
        if (exists $proph_prots{$Subj_id}){
                $Flag1="Proph";
                $Flag2="Phage";
        }
        elsif (exists $euk_prots{$Subj_id}){
                $Flag1="Euk";
                $Flag2="Euk"
        }
        elsif(exists $vir_prots{$Subj_id}){
                $Flag1="Vir";
                $Flag2="Phage";
        }
        else {
                $Flag1="Bact";
                $Flag2="Bact";
        }
        return($Flag1,$Flag2);
}

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In reply to Re^2: help with hash or arrays or hash references by AWallBuilder
in thread help with hash or arrays or hash references by AWallBuilder

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