#!/usr/bin/env perl
use strict;
use warnings;

my @a;
my $n = "\n";
@a = glob ("*.Recip.blast.top");
my $t = "\t";
foreach my $a (@a) {
    my @b = split (/[.]/, $a);
    my $OrginalBlast;
    $OrginalBlast =
        $b[0] . "."
      . $b[1] . "."
      . $b[2] . "."
      . $b[3] . "."
      . $b[4] . "."
      . $b[5] . "."
      . $b[6] . "."
      . $b[7];

#####ORGN is = AB|||||||

    open (ORGN, "/home/ajl12013/Labwork/Dbfiles/results/$OrginalBlast") || die;

######RECI is = BA|||||||

    open (RECI,   $a)                  || die;
    open (OUTM,   ">MatchingGI.txt")   || die;
    open (OUTNoM, ">NoMatchingGI.txt") || die;
    my $ORGN = <ORGN>;
    my $RECI = <RECI>;
    my %GenomeTable;
    my $Genome1A;
    my $G1A;
    my $data;
    my $G2A;
    my $Genome2A;
    my $l;
    local $/;
    my $key;
    $GenomeTable{$OrginalBlast} = $a;

#### First while statement for the AB file.
    $GenomeTable{$n} = $n;

    while (my $G1A = <ORGN>) {
        if ($G1A =~ m/^[gi|]\w/) {
            ($Genome1A) = $G1A =~ m/^gi\|\d+/g;
            $GenomeTable{$Genome1A} = [];
            $GenomeTable{$n};
            foreach my $keys (keys %GenomeTable) { print " Keys: $keys $n"; }
        }
        while ($G2A = $RECI) {
            if ($G2A =~ m/^[gi|]/) {
                $G2A =~ m/^gi\|\w+\|\w+\|\w+\.\d\|\w+\s(gi\|\d+)/g;
                $Genome2A = $1;
                $GenomeTable{$Genome1A} = $Genome2A;
                foreach my $values (values %GenomeTable) {
                    print "Values: $values $n";
                }

                $Genome1A eq $Genome2A
                  ? print OUTM $a . $n
                  : print OUTNoM $a . $n;

            }
        }
    }
}