#connect explicitely using the DBAdaptor
# (used in examples 1-8)

use Bio::EnsEMBL::DBSQL::DBAdaptor;
my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
		    -host   => 'ensembldb.ensembl.org',
                    -dbname => 'homo_sapiens_core_42_36b',
                    -user   => 'anonymous',
					    );

#OR connect automaticall using a the Registry
# (used in example 9)
#please see 
  http://www.ensembl.org/info/software/registry/index.html

use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
		   -host    => 'ensembldb.ensembl.org',
		   -user    => 'anonymous'
		   );

# [connect (1)]

my $chrom  = "X";
my $slice_adaptor = $db->get_SliceAdaptor;
my $slice = $slice_adaptor->fetch_by_region("chromosome", $chrom);
print "\nhave slice of ".$slice->seq_region_name." ".
      $slice->seq_region_start."-".$slice->seq_region_end;

# [connect (1)]

my $chrom  = "X";
my $start  = 100000;
my $end    = 200000;
my $strand = 1;
my $slice_adaptor = $db->get_SliceAdaptor;
my $slice = $slice_adaptor->fetch_by_region(
				"chromosome",
				$chrom,
				$start,
				$end,
				$strand);
print "\nhave slice of ".$slice->seq_region_name." ".
    $slice->seq_region_start."-".$slice->seq_region_end;

# [connect (1)]

my @chromosomes;
foreach my $chr ( @{ $slice_adaptor->fetch_all('chromosome') } ) {
   #print out information
   print $chr->seq_region_name.", ".$chr->start." - ".$chr->end."\n";
   #store the names
   push @chromosomes, $chr->seq_region_name;
   #or work with the chromosome...
}

# [connect (1)]

#all genes from a slice, e.g. a chromosome
# [get_slice]
my @genes = @{ $slice->get_all_Genes() };

#specific gene, using EnsEMBL-ID
my $gene_adaptor = $db->get_GeneAdaptor;
my $gene = $gene_adaptor->fetch_by_stable_id("ENSG00000147892");

#specific gene, using gene symbol (short name)
my $gene_adaptor = $db->get_GeneAdaptor;
my @genes = @{$gene_adaptor->fetch_all_by_external_name("ADAMTSL1")};

# [connect (1)]

# [get_gene (5)]

#print basic information
print "genomic localization:\t".$gene->seq_region_name.
      "\t".$gene->start."\t".$gene->end.
      "\t".$gene->strand."\n";
print "description:\t".$gene->description."\n";
#print further infos, ids
foreach my $dbEntry ( @{ $gene->get_all_DBEntries } ) {
   if( $dbEntry->database eq "HUGO" or
       $dbEntry->database eq ""){
      $symbol = "symbol:\t".$dbEntry->display_id."\n";
   }
   else{
      print "ID:\t".$dbEntry->database.":\t".
      	    $dbEntry->display_id."\n";
   }
}

# [connect (1)]

# [get_gene (5)]

foreach my $transcript ( @{ $gene->get_all_Transcripts } ) {
   print $transcript->dbID."\t".$transcript->start."\t".
   	 $transcript->end."\t".$transcript->strand."\n";
   foreach my $exon ( @{ $transcript->get_all_Exons } ) {
      print "\t".$exon->dbID."\t".$exon->start."\t".
      	    $exon->end."\n";
   }
}

# [connect (1)]

my $query = "SELECT gene_id, seq_region_id, seq_region_start,
	  seq_region_end, seq_region_strand FROM gene LIMIT 5;";
my $sth = $db->dbc->prepare($query);
$sth->execute();
while(my ($id, $region, $start, $end, $strand) = $sth->fetchrow) {
   print "gene $id: $region, $start, $end, $strand\n";
}

use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;

#use Registry file for a simple connection setup,
#please see 
  http://www.ensembl.org/info/software/registry/index.html
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
		-host    => 'ensembldb.ensembl.org',
		-user    => 'anonymous'
		);

#get compara adaptors
my $ma =  Bio::EnsEMBL::Registry->get_adaptor(
			'compara', 'compara', 'Member')
   or die "\n$@\ncan't get adaptor 1.\n";
my $ha =  Bio::EnsEMBL::Registry->get_adaptor(
			'compara', 'compara', 'Homology')
   or die "\n$@\ncan't get adaptor 2.\n";

#fetch human gene from core database
my $query_species = "Homo_sapiens";
my $gene_id       = "ENSG00000147892";

#fetch source gene
my $member = $ma->fetch_by_source_stable_id(
		"ENSEMBLGENE", $gene_id) or return 0;
my $sourceGenome = $member->genome_db->dbID;
print "\nsource gene ($query_species): ".$member->stable_id;

#get all homologues from other species
my $other_species = "Mus_musculus";
my $homologies = $ha->fetch_by_Member_paired_species(
			$member, $other_species);

#or from all species
#my $homologies = $ha->fetch_by_Member($member);

#display all results
foreach my $homologie (@$homologies) {
  foreach my $member_attrib (@{$homologie->get_all_Member_Attribute}) {
    my ($newmember, $attrib) = @$member_attrib;

    if ($newmember->genome_db->dbID != $sourceGenome) {
      print "\nhomologue: ".$newmember->stable_id.
      	    " / ".$newmember->taxon_id.
            ": ".$newmember->chr_name.
            " ".$newmember->chr_start.
            "-".$newmember->chr_end;
    }
  }
}

use Bio::EnsEMBL::DBSQL::DBAdaptor;
# [connect (1)]

#use GO::AppHandle for GO logic if possible!
use GO::AppHandle;
my %args = (
      -dbhost => 'sin.lbl.gov',
      -dbname => 'go',
	);
my $apph = GO::AppHandle->connect( \%args );

# [get_gene (5)]

#get GO infos
if ( $gene->is_known ) {
  foreach $link ( @{ $gene->get_all_DBLinks } ) {
    if ( $link->database eq "GO" ) {

      #show GO term
      print $link->display_id;

      #get the ancester terms
      foreach my $go (@GOs1) {
	get_parent($go);
      }

    }
  }
}

#fetch all parent terms recursively
sub get_parent($) {
  my $term = shift;
  my $parent_term;
  my $type;
  my $parent_terms;

  $parent_terms = $apph->get_parent_terms($term);
  foreach $parent_term (@$parent_terms) {
    get_parent($parent_term);
  }
  $parent_term = $term->name();
  if ( ( $parent_term ne "Gene_Ontology" )
        && ( $parent_term ne "molecular_function" )
	&& ( $parent_term ne "cellular_component" )
	&& ( $parent_term ne "biological_process" ) ) {
      print $parent_term."(".$term->type "), ";
  }
}