use strict;

my @bases;
my @list;
my @List;
my %oligo = ();
my %pos = ();
my $base;
my $list;
my $f;
my $nomefile;
my $line;
my $piece;
my $query;
my $len;
my $sequenza;
my $i;
my $j;
my $rev;
my $revcomp;
my $oligo;
my $length = length($sequenza);
my $piececomp;


print("Insert query:\n");
$query = <STDIN>;

chomp($query);

$len = length($query);

$query = uc $query;


@bases = qw(A G C T); #bases
@list = qw(A G C T);  #seed


for ($i = 0; $i < ($len - 1); $i++) 
{
    foreach $base (@bases)
	{
         foreach $list (@list)
		 {
            $oligo{$base.$list} = 1;
         }
		 
    @List = keys %oligo; 
	
    }
	
  @list = keys %oligo;
  
  %oligo = ();
  
    #print "@list   xxx \n";             
} 

%oligo = ();
@List = sort @List;



$nomefile = $ARGV[0];

open $f, "< $nomefile" or die "cannot open $nomefile: $!";

$line = <$f>;
chomp($line);

if(substr($line,0,1) ne ">")
{
 print STDERR ("Input file $nomefile not in FASTA format\n");
 exit;
 }



$sequenza = <$f>;


while($line = <$f>)
{
	chomp($line);	
	
	if(substr($line, 0, 1) ne ">")
	{
		$sequenza = $sequenza.$line;
	}
	
 	
}

$sequenza = uc $sequenza;



for($i = 0; $i < length($sequenza) - ($len - 1); $i++) # nell'ultimo frame di lettura non deve contare la len intera se no va 'fuori sequenza' e non trova l'oligo corrispondente
{

 $piece = substr($sequenza, $i, $len);

 if(exists $oligo{$piece})
  {
	 $oligo{$piece} = $oligo{$piece} + 1;
	 push(@{$pos{$piece}} , $i );
  }
 else
  {
	$oligo{$piece} = 1;
	push(@{$pos{$piece}} , $i );
	
  }
  
}


foreach $piece (sort keys %oligo)
{
 print("$piece\t$oligo{$piece}\t@{$pos{$piece}}\n\n");
}


$rev= reverse $query;
$rev=~ tr/ACTG/TGAC/;
$revcomp = $rev;


for($j = $length; $j < $length - $len; $j--) 
{	

	$revcomp = substr($sequenza, $j, $len);
 

	if(exists $oligo{$revcomp})
	{
		push(@{$pos{$revcomp}} , ($length - $j) - ($len - 1));
  	}
 
}
  

if(exists $oligo{$query} && !exists $oligo{$revcomp}) 
 {
	print("$query\t compare $oligo{$query} volte\t in posizione @{$pos{$query}} solo sul filamento positivo\n");
 }
 else
 {		
	if(exists $oligo{$query} && exists $oligo{$revcomp})
	{
		print("$query\t compare $oligo{$query} volte\t in posizione @{$pos{$query}} sul filamento positivo\n\ne compare $oligo{$revcomp} volte\t in posizione @{$pos{$revcomp}}\t  sul filamento negativo\n");
	}
	else
	{	
		if(!exists $oligo{$query} && exists $oligo{$revcomp})
		{
			print("$query compare $oligo{$revcomp} volte\t in posizione @{$pos{$revcomp}}\t sul filamento negativo\n");
		}
		else
		{
			print("$query non compare nella sequenza\n");
		}
	}
 }