##################
# Make connection with Ensembl, and retrieve start, end  and rank.
##################


my $datasource = "DBI:mysql:homo_sapiens_core_23_34e:ensembldb.ensembl.org";
my $dbh=();
my $sth=();  # database and statement handles
my @rows;         # to get results or queries
my $row_count;    # to see how much we get back
my $username = "anonymous";
my $password = "";
my $marker = 'marker_list.txt';

# connect to database:
$dbh = DBI->connect($datasource, $username, $password, {RaiseError => 1});

open (LIST, "<$marker") or die ("Couldn't open file $marker: $!.\n");

while (<LIST>){
    my ($ensemblID, $score) = $_;


    # select all sequence entries:

    $row_count = 0;
    $sth = $dbh->prepare (qq{
        SELECT gene_stable_id.stable_id, gene.seq_region_start, gene.seq_region_end, gene.seq_region_strand
        FROM gene, gene_stable_id
        WHERE gene_stable_id.gene_id = gene.gene_id
        AND gene_stable_id.stable_id ="$ensemblID"
    });
    $sth->execute ();

    # read results:
    while (@rows = $sth->fetchrow_array () ) {
        $row_count++;
        print join ("\t", @rows), "\n";
    }

    unless ( $row_count ) {
        print "This gene doesn't appear to be placed on the current assembly.\n";
    }

# tidy up:
close(LIST);
$sth->finish ();
$dbh->disconnect ();
}