Raw content of Bio::Das::ProServer::SourceAdaptor::conservation_score
<![CDATA[#
# Bio::Das::ProServer::SourceAdaptor::conservation_score
#
# Copyright EnsEMBL Team
#
# You may distribute this module under the same terms as perl itself
#
# pod documentation - main docs before the code
=head1 NAME
Bio::Das::ProServer::SourceAdaptor::conservation_score - Extension of the ProServer for e! conservation scores
=head1 INHERITANCE
This module inherits attributes and methods from Bio::Das::ProServer::SourceAdaptor
=head1 DAS CONFIGURATION FILE
There are some specific parameters for this module you can use in the DAS server configuration file
=head2 registry
Your registry configuration file to connect to the compara database
=head2 database
The species name in your Registry configuration file.
=head2 this_species
The main species. Features will be shown for this species.
=head2 other_species
The other species. This DAS track will show alignments between this_species and other_species.
You can add more than one other species separated by commas.
=head2 analysis
The method_link_type. This defines the type of score. E.g. GERP_CONSERVATION_SCORE
See perldoc Bio::EnsEMBL::Compara::MethodLinkSpeciesSet for more details about the
method_link_type
=head2 Example
=head3 registry configuration file
use strict;
use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-port => 3306,
-species => 'ensembl-compara-41',
-dbname => 'ensembl_compara_41');
=head3 DAS server configuration file
[general]
hostname = ecs4b.internal.sanger.ac.uk
prefork = 6
maxclients = 100
port = 9013
[conservation_score]
registry = /home/foo/ProServer/eg/reg.pl
state = on
adaptor = compara
database = ensembl-compara-41
this_species = Homo sapiens
other_species = Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus, Bos taurus, Monodelphis domestica
analysis = GERP_CONSTRAINED_ELEMENT
description = 7 way mlagan alignment
group_type = default
=cut
package Bio::Das::ProServer::SourceAdaptor::conservation_score;
use strict;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Exception;
use base qw( Bio::Das::ProServer::SourceAdaptor );
sub init
{
my ($self) = @_;
$self->{'capabilities'} = { 'features' => '1.0',
'stylesheet' => '1.0' };
my $registry = $self->config()->{'registry'};
unless (defined $registry) {
throw("registry not defined\n");
}
if (not $Bio::EnsEMBL::Registry::registry_register->{'seen'}) {
Bio::EnsEMBL::Registry->load_all($registry);
}
my $db = "Bio::EnsEMBL::Registry";
$db->no_version_check(1);
my $dbname = $self->config()->{'database'};
$self->{'compara'}{'meta_con'} =
$db->get_adaptor($dbname, 'compara', 'MetaContainer') or
die "no metadbadaptor:$dbname, 'compara','MetaContainer' \n";
$self->{'compara'}{'mlss_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'MethodLinkSpeciesSet') or
die "can't get $dbname, 'compara', 'MethodLinkSpeciesSet'\n";
$self->{'compara'}{'cs_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'ConservationScore') or
die "can't get $dbname, 'compara', 'ConservationScore'\n";
my $species = $self->config()->{'this_species'};
$self->{'compara'}{'slice_adaptor'} =
$db->get_adaptor($species, 'core', 'Slice') or
die "can't get $species, 'core', 'Slice'\n";
my $genome_db_adaptor =
$db->get_adaptor($dbname, 'compara', 'GenomeDB') or
die "can't get $dbname, 'compara', 'GenomeDB'\n";
$self->{'compara'}{'genomedbs'} = $genome_db_adaptor->fetch_all();
}
sub build_features
{
my ($self, $opts) = @_;
my $daschr = $opts->{'segment'} || return ( );
my $dasstart = $opts->{'start'} || return ( );
my $dasend = $opts->{'end'} || return ( );
my $species1 = $self->config()->{'this_species'};
my @other_species = split(/\s*\,\s*/, $self->config()->{'other_species'});
my $chr1 = $daschr;
my $start1 = $dasstart;
my $end1 = $dasend;
my $method_link = $self->config()->{'analysis'};
my $meta_con = $self->{'compara'}{'meta_con'};
my $stored_max_alignment_length;
my $values = $meta_con->list_value_by_key("max_alignment_length");
if(@$values) {
$stored_max_alignment_length = $values->[0];
}
my $mlss_adaptor = $self->{'compara'}{'mlss_adaptor'};
my $cs_adaptor = $self->{'compara'}{'cs_adaptor'};
my $slice_adaptor = $self->{'compara'}{'slice_adaptor'};
my $genomedbs = $self->{'compara'}{'genomedbs'};
my $species1_genome_db;
my @other_species_genome_dbs;
## Get the Bio::EnsEMBL::Compara::GenomeDB object for the primary species
foreach my $this_genome_db (@$genomedbs){
if ($this_genome_db->name eq $species1) {
$species1_genome_db = $this_genome_db;
}
}
if (!defined($species1_genome_db)) {
die "No species called $species1 in the database -- check spelling\n";
}
## Get the Bio::EnsEMBL::Compara::GenomeDB objects for the remaining species
foreach my $this_other_species (@other_species) {
my $this_other_genome_db;
foreach my $this_genome_db (@$genomedbs){
if ($this_genome_db->name eq $this_other_species) {
$this_other_genome_db = $this_genome_db;
last;
}
}
if (!defined($this_other_genome_db)) {
die "No species called $this_other_species in the database -- check spelling\n";
}
push(@other_species_genome_dbs, $this_other_genome_db);
}
## Fetch the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
my $method_link_species_set;
$method_link_species_set =
$mlss_adaptor->fetch_by_method_link_type_GenomeDBs(
$method_link, [$species1_genome_db, @other_species_genome_dbs]);
##Fetch the Bio::EnsEMBL::Slice object
my $slice = $slice_adaptor->fetch_by_region(undef, $chr1, $start1, $end1);
#Fetch conservation scores
my $conservation_scores = $cs_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($method_link_species_set, $slice);
## Build the results array
my @results = ();
foreach my $score (@$conservation_scores) {
my $id = $score->genomic_align_block_id;
my $label = "Conservation scores";
# note will contain expected and observed scores and window size
my $note = sprintf("Expected %.3f Observed %.3f Window Size %d Max", $score->expected_score, $score->observed_score, $score->window_size);
my $start_pos = $start1 + $score->position;
my $end_pos = $start1 + $score->position + $score->window_size;
my $new_score = $score->diff_score();
push @results, {
'id' => $id,
'label' => $label,
'method'=> $method_link,
'start' => $start_pos,
'end' => $end_pos,
'ori' => '+',
'score' => $new_score,
'note' => $note,
'typecategory' => 'Conservation scores',
'type' => 'Compara'
};
}
return @results;
}
sub das_stylesheet
{
my $self = shift;
return <<EOT;
<!DOCTYPE DASSTYLE SYSTEM "http://www.biodas.org/dtd/dasstyle.dtd">
<DASSTYLE>
<STYLESHEET version="1.0">
<CATEGORY id="Whole genome alignment">
<TYPE id="Compara">
<GLYPH>
<BOX>
<FGCOLOR>blue</FGCOLOR>
<BGCOLOR>aquamarine2</BGCOLOR>
</BOX>
</GLYPH>
</TYPE>
</CATEGORY>
</STYLESHEET>
</DASSTYLE>
EOT
}
1;
]]>