Bio::Das::ProServer::SourceAdaptor
compara
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Summary
Bio::Das::ProServer::SourceAdaptor::compara - Extension of the ProServer for e! genomic alignments
and synteny block.
Package variables
No package variables defined.
Included modules
Inherit
Bio::Das::ProServer::SourceAdaptor
Synopsis
No synopsis!
Description
No description!
Methods
| build_features | No description | Code |
| das_stylesheet | No description | Code |
| get_features_from_GenomicAlingBlocks | No description | Code |
| get_features_from_SyntenyRegions | No description | Code |
| init | No description | Code |
Methods description
None available.
Methods code
| build_features | description | prev | next | Top |
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 $link_template = $self->config()->{'link_template'} || '/';
$link_template .= '%s/contigview?chr=%s;vc_start=%d;vc_end=%d';
$self->{'compara'}->{'link_template'} = $link_template;
my $stored_max_alignment_length;
my $mlss_adaptor = $self->{'compara'}{'mlss_adaptor'};
my $dnafrag_adaptor = $self->{'compara'}{'dnafrag_adaptor'};
my $genomic_align_block_adaptor =
$self->{'compara'}{'genomic_align_block_adaptor'};
my $genomedbs = $self->{'compara'}{'genomedbs'};
my $species1_genome_db;
my @other_species_genome_dbs;
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";
}
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);
}
my $dnafrag1 =
$dnafrag_adaptor->fetch_by_GenomeDB_and_name($species1_genome_db, $chr1);
return ( ) if (!defined $dnafrag1);
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]);
my $features;
if ($method_link_species_set->method_link_class =~ /SyntenyRegion/) {
$features = $self->get_features_from_SyntenyRegions(
$method_link_species_set, $dnafrag1, $start1, $end1);
} else {
$features = $self->get_features_from_GenomicAlingBlocks(
$method_link_species_set, $dnafrag1, $start1, $end1);
}
return @$features;} | sub das_stylesheet
{
my $self = shift;
return <<EOT;
<!DOCTYPE DASSTYLE SYSTEM "http://www.biodas.org/dtd/dasstyle.dtd">
<DASSTYLE>
<STYLESHEET version="1.0">
<CATEGORY id="GenomicAlignBlock.pairwise_alignment">
<TYPE id="default">
<GLYPH>
<BOX>
<FGCOLOR>blue</FGCOLOR>
<BGCOLOR>aquamarine2</BGCOLOR>
</BOX>
</GLYPH>
</TYPE>
</CATEGORY>
<CATEGORY id="GenomicAlignBlock.multiple_alignment">
<TYPE id="default">
<GLYPH>
<BOX>
<FGCOLOR>brown</FGCOLOR>
<BGCOLOR>chocolate</BGCOLOR>
</BOX>
</GLYPH>
</TYPE>
</CATEGORY>
<CATEGORY id="GenomicAlignBlock.constrained_element">
<TYPE id="default">
<GLYPH>
<BOX>
<FGCOLOR>firebrick3</FGCOLOR>
<BGCOLOR>firebrick1</BGCOLOR>
</BOX>
</GLYPH>
</TYPE>
</CATEGORY>
<CATEGORY id="SyntenyRegion.synteny">
<TYPE id="default">
<GLYPH>
<BOX>
<FGCOLOR>black</FGCOLOR>
<BGCOLOR>DarkSeaGreen3</BGCOLOR>
</BOX>
</GLYPH>
</TYPE>
</CATEGORY>
</STYLESHEET>
</DASSTYLE>
EOT
}
1;} | | get_features_from_GenomicAlingBlocks | description | prev | next | Top |
sub get_features_from_GenomicAlingBlocks
{ my ($self, $method_link_species_set, $dnafrag1, $start1, $end1) = @_;
my $features = [];
my $genomic_align_block_adaptor = $self->{'compara'}{'genomic_align_block_adaptor'};
my $genomic_align_blocks = $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
$method_link_species_set, $dnafrag1, $start1, $end1);
my $group_coordinates;
foreach my $gab (@$genomic_align_blocks) {
my $group_id = $gab->group_id;
foreach my $genomic_align2 (@{$gab->get_all_non_reference_genomic_aligns()}) {
my $species_name = $genomic_align2->dnafrag->genome_db->name;
my $chr_name = $genomic_align2->dnafrag->name;
my $chr_start = $genomic_align2->dnafrag_start;
my $chr_end = $genomic_align2->dnafrag_end;
if (!defined($group_coordinates->{$group_id}->{$species_name}->{$chr_name})) {
$group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{start} = $chr_start;
$group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{end} = $chr_end;
} else {
if ($chr_start < $group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{start}) {
$group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{start} = $chr_start;
}
if ($chr_end > $group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{end}) {
$group_coordinates->{$group_id}->{$species_name}->{$chr_name}->{end} = $chr_end;
}
}
}
}
foreach my $gab (@$genomic_align_blocks) {
$genomic_align_block_adaptor->retrieve_all_direct_attributes($gab);
my $genomic_align1 = $gab->reference_genomic_align();
my $other_genomic_aligns = $gab->get_all_non_reference_genomic_aligns();
my $group_id = $gab->group_id;
my $id = $gab->dbID;
my $label;
my $group_label;
my $note = $gab->perc_id?$gab->perc_id.'% identity':undef;
my @links;
my @link_txts;
my @group_links;
my @group_link_txts;
foreach my $this_genomic_align (@{$gab->get_all_non_reference_genomic_aligns()}) {
my ($species2, $name2, $start2, $end2) = (
$this_genomic_align->dnafrag->genome_db->name(),
$this_genomic_align->dnafrag->name(),
$this_genomic_align->dnafrag_start(),
$this_genomic_align->dnafrag_end(),
);
my $ens_species = $species2;
$ens_species =~ s/ /_/g;
my $short_species2 = $species2;
$short_species2 =~ /(.)\S+\s(.{3})/;
$short_species2 = "$1.$2";
push(@links, sprintf($self->{compara}->{link_template}, $ens_species, $name2, $start2, $end2, $short_species2));
push(@link_txts, sprintf("%s:%s:%d-%d", $short_species2, $name2, $start2, $end2));
next if (!defined($group_id));
my $group_start2 = $group_coordinates->{$group_id}->{$species2}->{$name2}->{start};
my $group_end2 = $group_coordinates->{$group_id}->{$species2}->{$name2}->{end};
$group_label = "$name2: $group_start2-$group_end2";
push(@group_links, sprintf($self->{compara}->{link_template}, $ens_species, $name2,
$group_start2, $group_end2));
push(@group_link_txts, sprintf("%s:%s:%d-%d", $short_species2, $name2,
$group_start2, $group_end2));
}
if (@{$method_link_species_set->species_set} <= 2) {
my $ga = $gab->get_all_non_reference_genomic_aligns()->[0];
$label = $ga->dnafrag->name.": ".$ga->dnafrag_start."-".$ga->dnafrag_end;
} else {
$group_label = $group_id?"group $group_id":undef;
}
push @$features, {
'id' => $id,
'label' => $label,
'method'=> $method_link_species_set->method_link_type,
'start' => $genomic_align1->dnafrag_start,
'end' => $genomic_align1->dnafrag_end,
'ori' => ($genomic_align1->dnafrag_strand() == 1 ? '+' : '-'),
'score' => $gab->score(),
'note' => $note,
'link' => [@links],
'linktxt' => [@link_txts],
'group' => $group_id,
'grouplabel'=> $group_label,
'grouplink' => [@group_links],
'grouplinktxt' => [@group_link_txts],
'typecategory' => $method_link_species_set->method_link_class,
'type' => $method_link_species_set->name,
};
}
return $features;} | sub get_features_from_SyntenyRegions
{ my ($self, $method_link_species_set, $dnafrag1, $start1, $end1) = @_;
my $features = [];
my $synteny_region_adaptor = $self->{'compara'}{'synteny_region_adaptor'};
my $synteny_regions = $synteny_region_adaptor->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
$method_link_species_set, $dnafrag1, $start1, $end1);
my $data;
foreach my $this_synteny_region (@$synteny_regions) {
my $these_dnafrag_regions = $this_synteny_region->get_all_DnaFragRegions();
foreach my $this_dnafrag_region (@{$these_dnafrag_regions}) {
if ($this_dnafrag_region->genome_db->name == $dnafrag1->genome_db->name and
$this_dnafrag_region->dnafrag->name == $dnafrag1->name and
$this_dnafrag_region->dnafrag_start <= $end1 and
$this_dnafrag_region->dnafrag_end >= $start1) {
push(@$data, [$this_dnafrag_region, $these_dnafrag_regions]);
}
}
}
foreach my $this_data (@$data) {
my ($reference_dnafrag_region, $all_dnafrag_regions) = @$this_data;
my @links;
my @link_txts;
foreach my $this_dnafrag_region (@{$all_dnafrag_regions}) {
next if ($this_dnafrag_region == $reference_dnafrag_region);
my ($species2, $name2, $start2, $end2) = (
$this_dnafrag_region->dnafrag->genome_db->name(),
$this_dnafrag_region->dnafrag->name(),
$this_dnafrag_region->dnafrag_start(),
$this_dnafrag_region->dnafrag_end(),
);
my $ens_species = $species2;
$ens_species =~ s/ /_/g;
my $short_species2 = $species2;
$short_species2 =~ /(.)\S+\s(.{3})/;
$short_species2 = "$1.$2";
push(@links, sprintf($self->{compara}->{link_template}, $ens_species, $name2, $start2, $end2, $short_species2));
push(@link_txts, sprintf("%s:%s:%d-%d", $short_species2, $name2, $start2, $end2));
}
my $synteny_region_id = $reference_dnafrag_region->synteny_region_id;
push @$features, {
'id' => $synteny_region_id,
'label' => "Synteny Region #$synteny_region_id",
'method'=> $method_link_species_set->method_link_type,
'start' => $reference_dnafrag_region->dnafrag_start,
'end' => $reference_dnafrag_region->dnafrag_end,
'ori' => ($reference_dnafrag_region->dnafrag_strand() == 1 ? '+' : '-'),
'score' => '-',
'link' => [@links],
'linktxt' => [@link_txts],
'typecategory' => $method_link_species_set->method_link_class,
'type' => $method_link_species_set->name,
};
}
return $features;} | sub init
{
my ($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'}{'mlss_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'MethodLinkSpeciesSet') or
die "can't get $dbname, 'compara', 'MethodLinkSpeciesSet'\n";
$self->{'compara'}{'dnafrag_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'DnaFrag') or
die "can't get $dbname, 'compara', 'DnaFrag'\n";
$self->{'compara'}{'genomic_align_block_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'GenomicAlignBlock') or
die "can't get $dbname, 'compara', 'GenomicAlignBlock'\n";
$self->{'compara'}{'synteny_region_adaptor'} =
$db->get_adaptor($dbname, 'compara', 'SyntenyRegion') or
die "can't get $dbname, 'compara', 'SyntenyRegion'\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();} | General documentation
This module inherits attributes and methods from Bio::Das::ProServer::SourceAdaptor
| DAS CONFIGURATION FILE | Top |
There are some specific parameters for this module you can use in the DAS server configuration file
Your registry configuration file to connect to the compara database
The species name in your Registry configuration file.
The main species. Features will be shown for this species.
The other species. This DAS track will show alignments between this_species and other_species.
You will have to skip this one for self-alignments. You can add more than one other species
separated by comas.
The method_link_type. This defines the type of alignments. E.g. TRANSLATED_BLAT, BLASTZ_NET...
See perldoc Bio::EnsEMBL::Compara::MethodLinkSpeciesSet for more details about the
method_link_type
| registry configuration file | Top |
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');
| DAS server configuration file | Top |
[general]
hostname = ecs4b.internal.sanger.ac.uk
prefork = 6
maxclients = 100
port = 9013
[Hsap-Mmus-blastznet]
transport = ensembl
adaptor = compara
registry = /home/foo/ProServer/eg/reg.pl
state = on
database = ensembl-compara-41
this_species = Homo sapiens
other_species = Mus musculus
analysis = BLASTZ_NET
description = Human-mouse blastz-net alignments
[Mmus-Hsap-blastznet]
transport = ensembl
adaptor = compara
registry = /home/foo/ProServer/eg/reg.pl
state = on
database = ensembl-compara-41
this_species = Mus musculus
other_species = Homo sapiens
analysis = BLASTZ_NET
description = Mouse-Human blastz-net alignments
[primates-mlagan-hs]
transport = ensembl
adaptor = compara
registry = /home/foo/ProServer/eg/reg.pl
state = on
database = ensembl-compara-41
this_species = Homo sapiens
other_species = Pan troglodytes, Macaca mulatta
analysis = MLAGAN
description = Primates Mlagan alignments on human
[human-platypus-bz]
transport = ensembl
adaptor = compara
registry = /home/foo/ProServer/eg/reg.pl
state = on
database = ensembl-compara-41
this_species = Homo sapiens
other_species = Ornithorhynchus anatinus
analysis = BLASTZ_NET
description = Human-platypus blastz alignments