variation_density.pl

#
# calculates the variation density from given core database
# It finds Variation database by itself using naming convention s/core/variation/
#
#



use strict;

use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::DensityFeature;
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use Getopt::Long;

use Data::Dumper;
$Data::Dumper::Maxdepth = 2;

my $bin_count = 150;
my $long_slice_count = 100;

my ( $host, $user, $pass, $port, $dbname  );

my ( $block_count, $genome_size, $block_size );

GetOptions( "host=s", \$host,
	    "user=s", \$user,
	    "pass=s", \$pass,
	    "port=i", \$port,
	    "dbname=s", \$dbname
	  );


my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
					    -user => $user,
					    -port => $port,
					    -pass => $pass,
					    -dbname => $dbname,
					    -group => 'core',
					    -species => 'DEFAULT'
					   );

if( ! variation_attach( $db )) {
  die( "Couldnt attach variation to $dbname" );
}

#
# Get the adaptors needed;
#

my $dfa = $db->get_DensityFeatureAdaptor();
my $dta = $db->get_DensityTypeAdaptor();
my $aa  = $db->get_AnalysisAdaptor();
my $slice_adaptor = $db->get_SliceAdaptor();

my $top_slices = $slice_adaptor->fetch_all( "toplevel" );
my @sorted_slices =  sort { $b->seq_region_length() <=> $a->seq_region_length()} @$top_slices;



my $analysis = new Bio::EnsEMBL::Analysis (-program     => "variation_density.pl",
					   -database    => "ensembl",
					   -gff_source  => "variation_density.pl",
					   -gff_feature => "density",
					   -logic_name  => "snpDensity");

$aa->store( $analysis );