158256496-stool1_revised_C989779_1_gene1513     strand:+        203907.Bfl015   63.04   46      17      0       1       46      1       46      1e-07   59.3                                                       
158256496-stool1_revised_C989779_1_gene1513     strand:+        326427.Cagg_1194        65.22   46      16      0       2       47      3       48      1e-07   59.3                                               
158256496-stool1_revised_C989779_1_gene1513     strand:+        334413.FMG_1629 70.45   44      13      0       1       44      4       47      1e-07   59.3                                                       
158256496-stool1_revised_C989779_1_gene1513     strand:+        224915.bbp013   63.04   46      17      0       1       46      1       46      1e-07   59.3                                                       
158256496-stool1_revised_C989779_1_gene1513     strand:+        543302.AaLAA1DRAFT_2702 72.09   43      12      0       1       43      29      71      1e-07   59.3                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        484018.BACPLE_00501     77.43   505     114     0       1       505     1       505     0.0      848                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        547042.BACCOPRO_00289   77.43   505     114     0       1       505     5       509     0.0      848                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        449673.BACSTE_02782     77.56   508     111     1       1       505     1       508     0.0      847                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        665953.HMPREF1016_02618 77.76   508     110     1       1       505     1       508     0.0      845                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        762984.HMPREF9445_02115 77.17   508     113     1       1       505     1       508     0.0      845                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        702446.CUU_1632 77.03   505     116     0       1       505     1       505     0.0      845                                                       
158256496-stool1_revised_C989779_1_gene1517     strand:+        469593.HMPREF9011_00038 77.03   505     116     0       1       505     1       505     0.0      845                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        457394.BSFG_02153       77.03   505     116     0       1       505     1       505     0.0      845                                               
158256496-stool1_revised_C989779_1_gene1517     strand:+        435590.BVU_1475 77.03   505     116     0       1       505     1       505     0.0      845                     

##</code><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_prots, \%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);
}


##### For each Query_id find top bit score
my %top_bit;
        foreach my $key1 (sort keys %HoFlg2){
                foreach my $key2 (keys %{$HoFlg2{$key1}}){
                        print "key1\t$key1\tkey2$key2\tbitscore\t $HoFlg2{$key1}{$key2}\n"
                        $top_bit{$key1}=$HoFlg2{$key1}{$key2}; #??probably wrong
                }
         print "for query\t$key1 top bit score is\t$top_bit{$key1}\n";

        }