#!/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){
#  print $a."\n";
  my @b = split(/[.]/,$a);
  #print @b.$n;
  #print $b[0].$n.$b[1].$n.$b[2].$n.$b[3].$n.$b[4].$n.$b[5].$n.$b[6].$n.$b[7];
  my $OrginalBlast;
  $OrginalBlast = $b[0].".".$b[1].".".$b[2].".".$b[3].".".$b[4].".".$b[5].".".$b[6].".".$b[7];
#  print $OrginalBlast;
#  print $n;

#####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>;
  #The scalar format works here, but for some reason, the <RECI> doesnt print, this makes debugging the whole process very difficult and tedious.
  my $RECI = <RECI>;
  #print <ORGN>;
  #print "##############################################################################################";
  #print $RECI;
  #print <RECI>;
  my %GenomeTable;
my $Genome1A ;
  my $G1A;
  my $data;
  my $G2A;
  my $Genome2A;
  my $l;
  local $/;
  my $key;
$GenomeTable{$OrginalBlast} = $a ;

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

while(my $G1A = <ORGN>){
  # my @G1A = $G1A =~ m/^[gi]\d[|]$/g;
  #print $G1A;
  #print $G1A[0];
  #foreach my $q (@G1A){
  #  print $q
  #chomp($G1A);
  if ($G1A =~ m/^[gi|]\w/){
  ($Genome1A) = $G1A =~ m/^gi\|\d+/g;
  $GenomeTable{$Genome1A}  = [];
  $GenomeTable{$n};
  #print "These are the keys: ";
  #print  keys %GenomeTable ;
  #print $n;
#my $GenomeAB_ref;
#$GenomeAB_ref->$GenomeTable{$Genome1A};
#print $GenomeAB_ref;
  foreach my $keys (keys %GenomeTable){ print " Keys: $keys $n";}
}
 while($G2A = $RECI ){
    #print $G2A;
    #chomp($G2A);
    if($G2A =~ m/^[gi|]/){
      # print "Here";
       $G2A =~ m/^gi\|\w+\|\w+\|\w+\.\d\|\w+\s(gi\|\d+)/g;
      $Genome2A = $1;
       # ($l) = $G2A =~ m/^gi\|\d+/g;
     #$G2A =~ m/^gi\|\w+\|\w+\|\w+\.\d\|\w+\s(gi\|\d+)/g;
     #print $l;
     #$Genome2A = $1;
       #print $Genome2A;
    $GenomeTable{$Genome1A} = $Genome2A;
    #print "These are the valuesi: ";
    #print  values %GenomeTable   ;
    #print $n;
  foreach my $values (values %GenomeTable){print "Values: $values $n";}


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

  #exit;
}
#exit;
}
#exit;
}
}