use strict;


my $f;
my $nomefile;
my $line;

my %oligo = ();
my %pos = ();
my $piece;
my $query;
my $sequenza;
my $i;


$nomefile = $ARGV[0];

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

 

$sequenza = <$f>;

 

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

$sequenza = uc $sequenza;

 


for($i = 0; $i < length($sequenza) - 4; $i++)
{

 $piece = substr($sequenza, $i, 4);

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


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

 

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

chomp($query);

$query = uc $query;

if(exists $oligo{$query})
 {
 print("$query\t compare $oligo{$query} volte\t in posizione @{$pos{$query}}\n");
 }
 else
 {
    print("$query does not appear in the sequence");
 }