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Add homoeologues page and menu item - initially only for Triticum aes…
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modules/EnsEMBL/Web/Component/Gene/ComparaHomoeologs.pm
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| =head1 LICENSE | ||
| Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute | ||
| Licensed under the Apache License, Version 2.0 (the "License"); | ||
| you may not use this file except in compliance with the License. | ||
| You may obtain a copy of the License at | ||
| http://www.apache.org/licenses/LICENSE-2.0 | ||
| Unless required by applicable law or agreed to in writing, software | ||
| distributed under the License is distributed on an "AS IS" BASIS, | ||
| WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| See the License for the specific language governing permissions and | ||
| limitations under the License. | ||
| =cut | ||
|
|
||
| package EnsEMBL::Web::Component::Gene::ComparaHomoeologs; | ||
|
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||
| use strict; | ||
|
|
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| use HTML::Entities qw(encode_entities); | ||
|
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| use base qw(EnsEMBL::Web::Component::Gene); | ||
|
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| sub _init { | ||
| my $self = shift; | ||
| $self->cacheable(1); | ||
| $self->ajaxable(1); | ||
| } | ||
|
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||
| sub content { | ||
| my $self = shift; | ||
| my $hub = $self->hub; | ||
| my $object = $self->object; | ||
| my $species_defs = $hub->species_defs; | ||
| my $cdb = shift || $hub->param('cdb') || 'compara'; | ||
| my $availability = $object->availability; | ||
|
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| my @homoeologues = ( | ||
| $object->get_homology_matches('ENSEMBL_HOMOEOLOGUES', 'homoeolog', undef, $cdb), | ||
| ); | ||
|
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| my %homoeologue_list; | ||
| my %skipped; | ||
|
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| foreach my $homology_type (@homoeologues) { | ||
| foreach (keys %$homology_type) { | ||
| (my $species = $_) =~ tr/ /_/; | ||
| $homoeologue_list{$species} = {%{$homoeologue_list{$species}||{}}, %{$homology_type->{$_}}}; | ||
| $skipped{$species} += keys %{$homology_type->{$_}} if $hub->param('species_' . lc $species) eq 'off'; | ||
| } | ||
| } | ||
|
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| return '<p>No homoeologues have been identified for this gene</p>' unless keys %homoeologue_list; | ||
|
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| my %homoeologue_map = qw(SEED BRH PIP RHS); | ||
| my $alignview = 0; | ||
|
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| my ($html, $columns, @rows); | ||
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| my $column_name = $self->html_format ? 'Compare' : 'Description'; | ||
|
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| my $columns = [ | ||
| { key => 'Species', align => 'left', width => '10%', sort => 'html' }, | ||
| { key => 'Type', align => 'left', width => '5%', sort => 'string' }, | ||
| { key => 'dN/dS', align => 'left', width => '5%', sort => 'numeric' }, | ||
| { key => 'identifier', align => 'left', width => '15%', sort => 'html', title => $self->html_format ? 'Ensembl identifier & gene name' : 'Ensembl identifier'}, | ||
| { key => $column_name, align => 'left', width => '10%', sort => 'none' }, | ||
| { key => 'Location', align => 'left', width => '20%', sort => 'position_html' }, | ||
| { key => 'Target %id', align => 'left', width => '5%', sort => 'numeric' }, | ||
| { key => 'Query %id', align => 'left', width => '5%', sort => 'numeric' }, | ||
| ]; | ||
|
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| push @$columns, { key => 'Gene name(Xref)', align => 'left', width => '15%', sort => 'html', title => 'Gene name(Xref)'} if(!$self->html_format); | ||
|
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| @rows = (); | ||
|
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| foreach my $species (sort { ($a =~ /^<.*?>(.+)/ ? $1 : $a) cmp ($b =~ /^<.*?>(.+)/ ? $1 : $b) } keys %homoeologue_list) { | ||
| next if $skipped{$species}; | ||
|
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| foreach my $stable_id (sort keys %{$homoeologue_list{$species}}) { | ||
| my $homoeologue = $homoeologue_list{$species}{$stable_id}; | ||
| my ($target, $query); | ||
|
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| # (Column 2) Add in homoeologue description | ||
| my $homoeologue_desc = $homoeologue_map{$homoeologue->{'homology_desc'}} || $homoeologue->{'homology_desc'}; | ||
|
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| # (Column 3) Add in the dN/dS ratio | ||
| my $homoeologue_dnds_ratio = $homoeologue->{'homology_dnds_ratio'} || 'n/a'; | ||
|
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||
| # (Column 4) Sort out | ||
| # (1) the link to the other species | ||
| # (2) information about %ids | ||
| # (3) links to multi-contigview and align view | ||
| (my $spp = $homoeologue->{'spp'}) =~ tr/ /_/; | ||
| my $link_url = $hub->url({ | ||
| species => $spp, | ||
| action => 'Summary', | ||
| g => $stable_id, | ||
| __clear => 1 | ||
| }); | ||
|
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| # Check the target species are on the same portal - otherwise the multispecies link does not make sense | ||
| my $target_links = ($link_url =~ /^\// | ||
| && $cdb eq 'compara' | ||
| && $availability->{'has_pairwise_alignments'} | ||
| ) ? sprintf( | ||
| '<ul class="compact"><li class="first"><a href="%s" class="notext">Region Comparison</a></li>', | ||
| $hub->url({ | ||
| type => 'Location', | ||
| action => 'Multi', | ||
| g1 => $stable_id, | ||
| s1 => $spp, | ||
| r => undef, | ||
| config => 'opt_join_genes_bottom=on', | ||
| }) | ||
| ) : ''; | ||
|
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||
| if ($homoeologue_desc ne 'DWGA') { | ||
| ($target, $query) = ($homoeologue->{'target_perc_id'}, $homoeologue->{'query_perc_id'}); | ||
|
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| my $align_url = $hub->url({ | ||
| action => 'Compara_Homoeolog', | ||
| function => 'Alignment' . ($cdb =~ /pan/ ? '_pan_compara' : ''), | ||
| g1 => $stable_id, | ||
| }); | ||
|
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| unless ($object->Obj->biotype =~ /RNA/) { | ||
| $target_links .= sprintf '<li><a href="%s" class="notext">Alignment (protein)</a></li>', $align_url; | ||
| } | ||
| $align_url .= ';seq=cDNA'; | ||
| $target_links .= sprintf '<li><a href="%s" class="notext">Alignment (cDNA)</a></li>', $align_url; | ||
|
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| $alignview = 1; | ||
| } | ||
|
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| $target_links .= sprintf( | ||
| '<li><a href="%s" class="notext">Gene Tree (image)</a></li></ul>', | ||
| $hub->url({ | ||
| type => 'Gene', | ||
| action => 'Compara_Tree' . ($cdb =~ /pan/ ? '/pan_compara' : ''), | ||
| g1 => $stable_id, | ||
| anc => $homoeologue->{'gene_tree_node_id'}, | ||
| r => undef | ||
| }) | ||
| ); | ||
|
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| # (Column 5) External ref and description | ||
| my $description = encode_entities($homoeologue->{'description'}); | ||
| $description = 'No description' if $description eq 'NULL'; | ||
|
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| if ($description =~ s/\[\w+:([-\/\w]+)\;\w+:(\w+)\]//g) { | ||
| my ($edb, $acc) = ($1, $2); | ||
| $description .= sprintf '[Source: %s; acc: %s]', $edb, $hub->get_ExtURL_link($acc, $edb, $acc) if $acc; | ||
| } | ||
|
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| my @external = (qq{<span class="small">$description</span>}); | ||
|
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| if ($homoeologue->{'display_id'}) { | ||
| if ($homoeologue->{'display_id'} eq 'Novel Ensembl prediction' && $description eq 'No description') { | ||
| @external = ('<span class="small">-</span>'); | ||
| } else { | ||
| unshift @external, $homoeologue->{'display_id'}; | ||
| } | ||
| } | ||
|
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| my $id_info = qq{<p class="space-below"><a href="$link_url">$stable_id</a></p>} . join '<br />', @external; | ||
|
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| ## (Column 6) Location - split into elements to reduce horizonal space | ||
| my $location_link = $hub->url({ | ||
| species => $spp, | ||
| type => 'Location', | ||
| action => 'View', | ||
| r => $homoeologue->{'location'}, | ||
| g => $stable_id, | ||
| __clear => 1 | ||
| }); | ||
|
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| my $table_details = { | ||
| 'Species' => join('<br />(', split /\s*\(/, $species_defs->species_label($species)), | ||
| 'Type' => ucfirst $homoeologue_desc, | ||
| 'dN/dS' => $homoeologue_dnds_ratio, | ||
| 'identifier' => $self->html_format ? $id_info : $stable_id, | ||
| 'Location' => qq{<a href="$location_link">$homoeologue->{'location'}</a>}, | ||
| $column_name => $self->html_format ? qq{<span class="small">$target_links</span>} : $description, | ||
| 'Target %id' => $target, | ||
| 'Query %id' => $query | ||
| }; | ||
| $table_details->{'Gene name(Xref)'}=$homoeologue->{'display_id'} if(!$self->html_format); | ||
| push @rows, $table_details; | ||
| } | ||
| } | ||
| my $table = $self->new_table($columns, \@rows, { data_table => 1, sorting => [ 'Species asc', 'Type asc' ], id => 'homoeologues' }); | ||
| if ($alignview && keys %homoeologue_list) { | ||
| # PREpend | ||
| $html = sprintf( | ||
| '<p><a href="%s">View sequence alignments of all homoeologues</a>.</p>', | ||
| $hub->url({ action => 'Compara_Homoeolog', function => 'Alignment' . ($cdb =~ /pan/ ? '_pan_compara' : ''), }) | ||
| ).$html; | ||
| } | ||
|
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| $html .= $table->render; | ||
|
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| if (scalar keys %skipped) { | ||
| my $count; | ||
| $count += $_ for values %skipped; | ||
|
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| $html .= '<br />' . $self->_info( | ||
| 'homoeologues hidden by configuration', | ||
| sprintf( | ||
| '<p>%d homoeologues not shown in the table above from the following species. Use the "<strong>Configure this page</strong>" on the left to show them.<ul><li>%s</li></ul></p>', | ||
| $count, | ||
| join "</li>\n<li>", map "$_ ($skipped{$_})", sort keys %skipped | ||
| ) | ||
| ); | ||
| } | ||
| return $html; | ||
| } | ||
|
|
||
| 1; |
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