Thank you for the suggestion of the other way. I now check and if it is the first time it sees this query it will assign the current bit_score as the max, and then check all subsequent ones to see if they are bigger.

and maybe I'll re-read the llama book. It was a while ago and I left Perl for a few years, and seem to have a selective memory.

my $in_blast_tab=$ARGV[0];
open(IN,$in_blast_tab) or die "cannot open $in_blast_tab\n";

my $HoFlg1={}; my $HoFlg2={};
my %maxBits;
while (my $line=<IN>) {
        next if ($line =~ /^#/);
        next unless ($line =~ /\S/);
        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);
        if (!exists $maxBits{$Query_id}){
                $maxBits{$Query_id}=$bit_score;
        }
        elsif (exists $maxBits{$Query_id} && $bit_score > $maxBits{$Qu
+ery_id}){
                $maxBits{$Query_id}=$bit_score;
        }
        my ($Flag1, $Flag2 ) = &Flag( $Subj_id, \%proph_prots, \%euk_p
+rots, \%vir_prots );
        $HoFlg1->{$Query_id}->{$Flag1}->{$bit_score}++;
        $HoFlg2->{$Query_id}->{$Flag2}->{$bit_score}++;
        print join("\t",$Query_id,$Subj_id,"bit",$bit_score,"F1",$Flag
+1,"F2",$Flag2,"maxBits{Query}",$maxBits{$Query_id})."\n";

}
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