open (IN, "< D_radiodurans.faa");

while (<IN>) {
    chomp;

    if (/>(\S+)/) {
        $accession = $1;
	$description{$accession} = $_;
    }
}
close (IN);
open (X, "< X.out");
open (Y, "< Y.out");

while (<X>) {
    chomp;
    @a = split /\t/;
    $queryAccession = $a[0];
    $bitscore = $a[11];
    $xhit{$queryAccession} = $bitscore;
    $ahit{$queryAccession} = 1;
}
close (X);

while (<Y>) {
    chomp;
    @a = split /\t/;
    $queryAccession = $a[0];
    $bitscore = $a[11];
    $yhit{$queryAccession} = $bitscore;
    $ahit{$queryAccession} = 1;
}
close (Y);

foreach $queryAccession (keys %ahit) {
    if ($xhit{$queryAccession} == 0) {		#if no match in X, set score to zero
        $xhit{$queryAccession} = 0;
    }
    if ($yhit{$queryAccession} == 0) {		#if no match in Y, set score to zero
        $yhit{$queryAccession} = 0;
    }
    $xhit{$queryAccession} =~ s/ //g;		#remove spaces in my bitscores!?
    $yhit{$queryAccession} =~ s/ //g;
    $i++;
    print "$xhit{$queryAccession}\t$yhit{$queryAccession}\t$i\t$description{$queryAccession}\n";
}