use strict;
use warnings;

my $dir="./Im1107Rmapto06len90bp1miss1gap-2/";
my $DIR;
my $OUTDIR="./Im1107Runmapped05and06/";
mkdir $OUTDIR;
my $f;
my @lis=();
my $IN;
my $l="";
my $w="";

my %hash=();
my $dirref="./Im1107Runmapped05/";
my $DIRREF;
my $g;
my $r="";
my $z="";
my $OUT;
my $REF;
my $u="-unmapped05and06";

opendir $DIR,$dir or die "Error $dir\n";
while($f=readdir $DIR){
	if($f ne "." && $f ne ".." && $f=~ /^$w/){
		print "$f\n";
		open $IN,"<","$dir$f" or die "Error $IN\n";
		while($l=<$IN>){
			chomp $l; 
			@lis=split /\t/,$l; 
			$hash{">$lis[0]"}="peni16";
		}
		
	}
}
close $IN;
closedir $DIR;

opendir $DIRREF,$dirref or die "Error $dirref\n";
while($g=readdir $DIRREF){
	if($g ne "." && $g ne ".." && $g=~ /^$z/){
		print "$g\n";
		open $REF,"<","$dirref$g" or die "Error $REF\n";
		open $OUT,">","$OUTDIR$g$u.fasta";
		my $check=0;
		while($r=<$REF>){
			chomp $r;
			if($r=~ /^>.+/){
				$check=0;
				if(exists $hash{"$r"}){
				$check=1;
				}else{
					print $OUT "$r\n";
				}
			}elsif($check==0){
				print $OUT "$r\n";
			}
		}
		print "OK2";
		close $REF;
		close $OUT;
	}
}
print "OK3";
closedir $DIRREF;
print "OK4";
exit;