use warnings;

$userinput = <STDIN>;
chomp $userinput;
$basis_file = "/WINDOWS/jbproject/ZNF236/";
$basis_file .= $userinput;

open(BASIS, $basis_file) || die "Couldn't open BasisFile.\n";
@sequence_basis = <BASIS>;

foreach $sequence (@sequence_basis)
{
$sequence_temp .= $sequence;
}

#Falsche Zeichen löschen
$sequence_temp =~ s/[\s0-9]//g;
$sequence_temp =~ tr/a-z/A-Z/;
$sequence1 = reverse $sequence_temp;
$len_sequence1 = length $sequence1;
$use_length = $len_sequence1;

#arrays


print "\nLength Seq1:";
print $len_sequence1;
print "\n";

#open output-file
open(OUTPUT, ">/WINDOWS/jbproject/ZNF236/output.txt") || die "Couldn't open Output.\n";
print OUTPUT "---------------------------\n";
print OUTPUT $basis_file;
print OUTPUT "\n";


# open intronpool-table
open(INTRONPOOL, "/WINDOWS/jbproject/ZNF236/IntronPool.txt") || die "Couldn't open IntronPool.\n";
@answer1 = <INTRONPOOL>;

for $line (@answer1) 
{
$open_file_complete = $line;
chomp($open_file_complete);

$open_file = "/WINDOWS/jbproject/ZNF236/";
$open_file .=  $open_file_complete;
print $open_file;
print "\n";

	#open intron-file
	$intron_sequence_temp = "";
	open(INTRONFILE, $open_file) || die "Couldn't open IntronFile.\n";
	@intron_sequence_basis = <INTRONFILE>;
	$intron_sequence = "";
	foreach $intron_sequence (@intron_sequence_basis)
	{
	$intron_sequence_temp .= $intron_sequence;
	}

	$intron_sequence_temp =~ s/[\s0-9]//g;
	$intron_sequence_temp =~ tr/a-z/A-Z/;
	$intron_sequence_complete = reverse $intron_sequence_temp;
	$len_intron_sequence = length $intron_sequence_complete;
	if($len_intron_sequence < $len_sequence1) {$use_length = $len_intron_sequence;}
	print "\n $use_length";
	#comparison
	for ($position = 0; $position < $use_length; $position++) 
		{
		$nucleotide_basis= substr($sequence1, $position, 1);
		$nucleotide_file= substr($intron_sequence_complete, $position, 1);
		if($nucleotide_basis eq $nucleotide_file) 
			{
			 #print "Pos $position found $nucleotide_file in $userinput and $open_file_complete \n";
			 print OUTPUT "Pos $position found $nucleotide_file in $userinput and $open_file_complete \n";
			 $whereto = ">>/WINDOWS/jbproject/ZNF236/Pos/";
			 $whereto .= $position;
			 $whereto .= ".txt";
			 open(FOUND, $whereto) || die "Couldn't open WhereTo.\n";
			 print FOUND $nucleotide_file;
			 print FOUND "\n";
			 print FOUND $open_file;
			 $nucleic_vicinity= "";
			 $start_vicinity = 0;
			 $start_vicinity = $position;
			 $start_vicinity = $start_vicinity-5;
                         $nucleic_vicinity= substr($intron_sequence_complete, $start_vicinity, 11);
                         $nucleic_vicinity= reverse $nucleic_vicinity;
			 print FOUND "\n Forward:";
			 print FOUND $nucleic_vicinity;
			 print FOUND "\n";
			 print FOUND "\n";
			 close (FOUND);
			 $whereto = "";
			}
                }

close (INTRONFILE);
$use_length = $len_sequence1;
$nucleotide_basis = "";
$nucleotide_file = "";
}
print OUTPUT "\n ---------------------------\n";
close (OUTPUT);
close (INTRONPOOL);
close (BASIS);