############### 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;
my %maxBits; my $max_bits=60;

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",$line); # extra f
ield of strand
        next if ($bit_score <60);
        if ($bit_score > $max_bits){
                $max_bits=$bit_score;
        }
        $maxBits{$Query_id}=$max_bits;
        my ($Flag1, $Flag2 ) = &Flag( $Subj_id, \%proph_prots, \%euk_prots, \%vir_prots );
        $HoFlg1->{$Query_id}->{$Flag1}->{$bit_score}++;
        $HoFlg2->{$Query_id}->{$Flag2}->{$bit_score}++;
        print join("\t",$Query_id,$Subj_id,$bit_score,$Flag1,$Flag2)."\n";
}
## Get a Flag for each query/subject 
sub Flag {
    my ( $Subj_id, $proph_prots, $euk_prots, $vir_prots ) = @_;
    return "Proph", "Phage" if exists $$proph_prots{$Subj_id};
    return "Euk",   "Euk"   if exists $$euk_prots{$Subj_id};
    return "Vir",   "Phage" if exists $$vir_prots{$Subj_id};
    return "Bact",  "Bact";
} ## end sub Flag

## now for all query/flag pairs with bit scores that are within 90% of the top_bit for that query
## 
my @flag_list2=("Phage","Euk","Bact");
my $count={};
foreach my $q (keys %{$HoFlg2}){
print "$q\t";
        for my $flag (@flag_list2){
                for my $b (keys %{$HoFlg2->{$flag}}){
                        if ($b > 0.9*$maxBits{$q}){
                                $count->{$flag} += $HoFlg2->{$q}->{$flag}->{$b};
                        }

                }
        print "$count\t";
        }
print "\n";
}