Take the strain, disentangle clustersets (#1093)

Author: twalsh-ebi

modules/EnsEMBL/Web/Component/Gene/ComparaOrthologs.pm

@@ -23,6 +23,7 @@ use strict;
 
 use HTML::Entities qw(encode_entities);
 
+use EnsEMBL::Web::Utils::Compara qw(orthoset_prod_names);
 use EnsEMBL::Web::Utils::FormatText qw(glossary_helptip get_glossary_entry pluralise);
 
 use base qw(EnsEMBL::Web::Component::Gene);
@@ -46,8 +47,9 @@ sub content {
   my $biotype      = $object->Obj->get_Biotype;  # We expect a Biotype object, though it could be a biotype name.
   my $is_ncrna     = ( ref $biotype eq 'Bio::EnsEMBL::Biotype' ? $biotype->biotype_group =~ /noncoding$/ : $biotype =~ /RNA/ );
   my $species_name = $species_defs->GROUP_DISPLAY_NAME;
-  my $strain_url   = $hub->is_strain ? "Strain_" : "";
-  my $strain_param = $hub->is_strain ? ";strain=1" : ""; # initialize variable even if is_strain is false, to avoid warnings
+  my $is_strain_view = $hub->action =~ /^Strain_/ ? 1 : 0;
+  my $strain_url   = $is_strain_view ? "Strain_" : "";
+  my $strain_param = $is_strain_view ? ";strain=1" : ""; # initialize variable even if is_strain_view is false, to avoid warnings
 
   my @orthologues = (
     $object->get_homology_matches('ENSEMBL_ORTHOLOGUES', undef, undef, $cdb), 
@@ -78,11 +80,14 @@ sub content {
     delete $compara_species->{'ancestral_sequences'};
   }
 
+  my $orthoset_prod_names = EnsEMBL::Web::Utils::Compara::orthoset_prod_names($hub, $cdb, $is_strain_view);
+  my $orthoset_prod_name_set = {map {$_ => 1} @$orthoset_prod_names};
+
   ## Work out which species we want to skip over, based on page type  and user's configuration
   my $this_group        = $species_defs->STRAIN_GROUP;
   my $species_not_shown = {}; 
-  my $strains_not_shown = {};
-  my $strain_refs       = {};
+  my $species_not_relevant = {};
+  my $unshown_strain_types = {};
   my $hidden            = {};
 
   foreach my $prod_name (keys %$compara_species) {
@@ -92,30 +97,23 @@ sub content {
     next if $species eq $hub->species; ## Ignore current species
     my $label = $is_pan ? $pan_lookup->{$prod_name}{'display_name'} : $species_defs->species_label($species);
 
-    ## Should we be showing this orthologue on this pagpe by default?
-    my $strain_group  = $species_defs->get_config($species, 'STRAIN_GROUP');
-    my $related_taxon = $species_defs->get_config($species, 'RELATED_TAXON');
-    if ($hub->action =~ /^Strain_/) {
-      unless (($strain_group && $strain_group eq $this_group) || ($related_taxon && $related_taxon eq $species_defs->RELATED_TAXON)) {
-        $species_not_shown->{$species} = $label;
-        next;
-      }
-    }
-    else {
-      if ($strain_group) {
-        if ($strain_group eq $prod_name) {
-          $strain_refs->{$species} = $label;
-        }
-        else { 
-          ## Do not show any strain species on main species view
-          $strains_not_shown->{$species} = $label;
-          next;
-        }
-      }
+    # Should we be showing this orthologue on this page by default?
+    unless ($orthoset_prod_name_set->{$prod_name}) {
+      $species_not_relevant->{$species} = 1;
+      next;
     }
 
     ## Do we even have an orthologue for this species?
     unless ($orthologue_list{$species}) {
+
+      my $strain_group = $species_defs->get_config($species, 'STRAIN_GROUP');
+      my $strain_type = $strain_group && $prod_name ne $strain_group
+                      ? $species_defs->get_config($species, 'STRAIN_TYPE')
+                      : 'species'
+                      ;
+
+      $unshown_strain_types->{$strain_type} += 1;
+
       $species_not_shown->{$species} = $label;
       next;
     }
@@ -200,8 +198,8 @@ sub content {
   my $anc_node_ids = $self->fetch_anc_node_ids($cdb);
   foreach my $species (sort { ($a =~ /^<.*?>(.+)/ ? $1 : $a) cmp ($b =~ /^<.*?>(.+)/ ? $1 : $b) } keys %orthologue_list) {
     next unless $species;
+    next if $species_not_relevant->{$species};
     next if $species_not_shown->{$species};
-    next if $strains_not_shown->{$species};
     next if $hidden->{$species};
 
     my ($species_label, $prodname);
@@ -367,29 +365,26 @@ sub content {
     );
   }   
 
-  if (($hub->action =~ /^Strain_/ && keys %$strains_not_shown)
-    || ($hub->action !~ /^Strain_/ && keys %$species_not_shown)) {
-    my ($total, $no_ortho_species, $strain_refs_html);
-    if ($hub->action =~ /^Strain_/) {
-      $total = scalar keys %$strains_not_shown; 
-      $no_ortho_species = $self->get_no_ortho_species_html($strains_not_shown, $sets_by_species);
-      $strain_refs_html = '';
-    }
-    else {
-      $total = scalar keys %$species_not_shown; 
-      unless ($is_pan) {
-        $no_ortho_species = $self->get_no_ortho_species_html($species_not_shown, $sets_by_species);
-        $strain_refs_html = $self->get_strain_refs_html($strain_refs, $species_not_shown);
-      }
+  if (keys %$species_not_shown) {
+    my $no_ortho_species;
+    my $total = scalar keys %$species_not_shown;
+    unless ($is_pan) {
+      $no_ortho_species = $self->get_no_ortho_species_html($species_not_shown, $sets_by_species);
     }
     my $not_shown_list = $is_pan ? '' : sprintf('<ul id="no_ortho_species">%s</ul>', $no_ortho_species);
+    my $strain_type_breakdown = $self->get_strain_type_breakdown($unshown_strain_types, $total);
+
+    my $not_shown_desc = $total > 1
+                       ? "are not shown in the table above because they don't have any orthologue with"
+                       : "is not shown in the table above because it doesn't have any orthologue with"
+                       ;
+
     $html .= '<br /><a name="list_no_ortho"/>' . $self->_info(
       'Species without orthologues',
       sprintf(
-        qq(<p><span class="no_ortho_count">%d</span> species are not shown in the table above because they don't have any orthologue with %s.</p>
+        qq(<p><span class="no_ortho_count">%d</span> %s %s %s.</p>
 %s
-%s
-</p> <input type="hidden" class="panel_type" value="ComparaOrtholog" />), $total, $self->object->Obj->stable_id, $not_shown_list, $strain_refs_html),
+</p> <input type="hidden" class="panel_type" value="ComparaOrtholog" />), $total, $strain_type_breakdown, $not_shown_desc, $self->object->Obj->stable_id, $not_shown_list),
       undef,
       'no_ortho_message_pad'
     );
@@ -410,7 +405,7 @@ sub create_gene_tree_links {
   my $orthologue = $params->{orthologue};
 
   my $hub          = $self->hub;
-  my $strain_url   = $hub->is_strain ? "Strain_" : "";
+  my $strain_url   = $hub->action =~ /^Strain_/ ? "Strain_" : "";
 
   my $tree_url = $hub->url({
     type   => 'Gene',
@@ -432,32 +427,23 @@ sub species_sets {
   my $hub             = $self->hub;
   my $species_defs    = $hub->species_defs;
   my $is_pan          = $cdb =~ /compara_pan_ensembl/;
+  my $is_strain_view  = $self->hub->action =~ /^Strain_/;
 
-  return "" if $self->hub->action =~ /^Strain/; #No summary table needed for strains
+  return "" if $is_strain_view; #No summary table needed for strains
 
   my ($set_order, $species_sets, $set_mappings) = $self->species_set_config($cdb);  #setting $cdb enables us to fetch Pan species sets
 
   return "" unless $set_order;
 
-  my $compara_spp     = {};
+  my $compara_spp     = EnsEMBL::Web::Utils::Compara::orthoset_prod_names($hub, $cdb, $is_strain_view);
   my $lookup          = $species_defs->prodnames_to_urls_lookup($cdb);
-  my $pan_info        = {};
-  if ($is_pan) {
-    $pan_info = $species_defs->multi_val('PAN_COMPARA_LOOKUP');
-    $compara_spp = {map { $_ => 1} keys %$pan_info};
-  }
-  else {
-    $compara_spp = { %{$species_defs->multi_hash->{'DATABASE_COMPARA'}{'COMPARA_SPECIES'}} };
-    delete $compara_spp->{'ancestral_sequences'};
-  }
+  my $pan_info        = $is_pan ? $species_defs->multi_val('PAN_COMPARA_LOOKUP') : {};
   my %orthologue_map  = qw(SEED BRH PIP RHS);
   my $sets_by_species = {};
   my $ortho_type      = {};
 
-  foreach (keys %$compara_spp) {
+  foreach (@$compara_spp) {
     my $species = $lookup->{$_};
-    next unless $species; #skip species absent from URL lookup (e.g. Human in Ensembl Plants)
-    next if $self->hub->is_strain($species); #skip strain species
 
     my $orthologues = $orthologue_list->{$species} || {};
     my $no_ortho = 0;
@@ -503,7 +489,7 @@ sub species_set_config {} # Stub, as it's clade-specific - implement in plugins
 
 sub fetch_anc_node_ids {}  # Another stub, only for specific divisions (e.g. Metazoa)
 
-sub get_strain_refs_html {
+sub get_strain_refs_html {  # not in use as of 2025-06
   my ($self, $strain_refs, $species_not_shown) = @_;
   return '' unless keys %{$strain_refs||{}};
 
@@ -532,14 +518,33 @@ sub get_no_ortho_species_html {
   my $hub = $self->hub;
   my $html = '';
 
-  foreach (sort {lc $a cmp lc $b} keys %$species_not_shown) {
+  # Species will be easier to find if we sort them by display name.
+  foreach (sort {lc $species_not_shown->{$a} cmp lc $species_not_shown->{$b}} keys %$species_not_shown) {
     my $class = $sets_by_species->{$_} ? sprintf(' class="%s"',  join(' ', @{$sets_by_species->{$_}})) : '';
     $html .= sprintf '<li%s>%s</li>', $class, $species_not_shown->{$_};
   }
 
   return $html;
 }
 
+sub get_strain_type_breakdown {
+## Get text listing strain types in order of decreasing frequency.
+  my ($self, $strain_types, $num_genomes) = @_;
+
+  my @ordered_strain_types = sort {$strain_types->{$b} <=> $strain_types->{$a} || $a cmp $b} keys %$strain_types;
+
+  if ($num_genomes > 1) {
+    @ordered_strain_types = map { pluralise($_) } @ordered_strain_types;
+  }
+
+  my $strain_type_text = scalar(@ordered_strain_types) > 1
+                       ? join(', ', @ordered_strain_types[0 .. ($#ordered_strain_types-1)]) . ' and ' . $ordered_strain_types[-1]
+                       : $ordered_strain_types[0]
+                       ;
+
+  return $strain_type_text;
+}
+
 sub get_export_data {
 ## Get data for export
   my ($self, $flag) = @_;

modules/EnsEMBL/Web/Component/Gene/ComparaParalogs.pm

@@ -42,7 +42,7 @@ sub content {
   my $cdb            = shift || $hub->param('cdb') || 'compara';
   my $biotype        = $self->object->Obj->get_Biotype;  # We expect a Biotype object, though it could be a biotype name.
   my $is_ncrna       = ( ref $biotype eq 'Bio::EnsEMBL::Biotype' ? $biotype->biotype_group =~ /noncoding$/ : $biotype =~ /RNA/ );
-  my $strain_url     = $hub->is_strain ? 'Strain_' : '';
+  my $strain_url     = $hub->action =~ /^Strain_/ ? 'Strain_' : '';
   my %paralogue_list = %{$self->object->get_homology_matches('ENSEMBL_PARALOGUES', 'paralog|gene_split', undef, $cdb)};
 
   return '<p>No paralogues have been identified for this gene</p>' unless keys %paralogue_list;

modules/EnsEMBL/Web/Component/Gene/ComparaTree.pm

@@ -38,7 +38,8 @@ sub get_details {
   my $member = $object->get_compara_Member({'stable_id' => $object->stable_id, 'cdb' => $cdb});
   return (undef, '<strong>Gene is not in the compara database</strong>') unless $member;
 
-  my $strain_tree  = $self->hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if ($self->hub->is_strain || $self->hub->param('strain') || $self->hub->action =~ /Strain_/);
+  my $strain_tree = $self->hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if ($self->hub->param('strain') || $self->hub->action =~ /^Strain_/);
+
   my $tree = $object->get_GeneTree($cdb,"", $strain_tree);
   return (undef, '<strong>Gene is not in a compara tree</strong>') unless $tree;
 
@@ -94,7 +95,7 @@ sub content {
   my $hub         = $self->hub;
   my $object      = $self->object || $self->hub->core_object('gene');
   my $is_genetree = $object && $object->isa('EnsEMBL::Web::Object::GeneTree') ? 1 : 0;
-  my $is_strain   = $hub->is_strain || $hub->param('strain') || $hub->action =~ /Strain_/;
+  my $is_strain_view = $hub->param('strain') || $hub->action =~ /^Strain_/;
   my ($gene, $member, $tree, $node);
 
   my $type   = $self->param('data_type') || $hub->type;
@@ -148,7 +149,7 @@ sub content {
   if (defined $parent) {
 
     if ($vc->get('super_tree') eq 'on' || $self->param('super_tree') eq 'on') {
-      my $super_url = $self->ajax_url('sub_supertree',{ cdb => $cdb, update_panel => undef, strain => $is_strain });
+      my $super_url = $self->ajax_url('sub_supertree',{ cdb => $cdb, update_panel => undef, strain => $is_strain_view });
       $html .= qq(<div class="ajax"><input type="hidden" class="ajax_load" value="$super_url" /></div>);
     } else {
       $html .= $self->_info(
@@ -163,10 +164,10 @@ sub content {
   }
 
   if ($hub->type eq 'Gene') {
-    if ($tree->tree->clusterset_id ne $clusterset_id && !$self->is_strain) {
+    if ($tree->tree->clusterset_id ne $clusterset_id) {
       $html .= $self->_info('Phylogenetic model selection',
         sprintf(
-          'The phylogenetic model <I>%s</I> is not available for this tree. Showing the default (consensus) tree instead.', $clusterset_id
+          'The phylogenetic model <i>%s</i> is not available for this tree. Showing the <i>%s</i> tree instead.', $clusterset_id, $tree->tree->clusterset_id,
           )
       );
     } elsif ($tree->tree->ref_root_id) {
@@ -280,7 +281,7 @@ sub content {
     image_width     => $image_width,
     slice_number    => '1|1',
     cdb             => $cdb,
-    strain          => $is_strain,
+    strain          => $is_strain_view,
   });
 
   # Keep track of collapsed nodes
@@ -393,7 +394,11 @@ sub content {
       my $collapsed_to_rank = $self->collapsed_nodes($tree, $node, "rank_$rank", $highlight_genome_db_id, $highlight_gene);
       push @rank_options, sprintf qq{<option value="%s" %s>%s</option>\n}, $hub->url({ collapse => $collapsed_to_rank, g1 => $highlight_gene, s1 => $highlight_species_url, gtr => $rank }), $rank eq $selected_rank ? 'selected' : '', ucfirst $rank;
     }
-    push @view_links, sprintf qq{<li>Collapse all the nodes at the taxonomic rank <select onchange="Ensembl.redirect(this.value)">%s</select></li>}, join("\n", @rank_options) if(!$self->is_strain);
+    # The ability to collapse by taxonomic rank was not seen as
+    # particularly useful in a strain gene-tree view ( ENSWEB-3037 ).
+    if(!$is_strain_view) {
+      push @view_links, sprintf qq{<li>Collapse all the nodes at the taxonomic rank <select onchange="Ensembl.redirect(this.value)">%s</select></li>}, join("\n", @rank_options);
+    }
   }
 
   $html .= $image->render;

modules/EnsEMBL/Web/Component/Gene/Compara_Portal.pm

@@ -35,8 +35,9 @@ sub content {
   my $hub           = $self->hub;
   my $availability  = $self->object->availability;
   my $location      = $hub->url({ type => 'Location',  action => 'Compara' });
-  my $strain_url    = ($self->is_strain || $hub->action =~ /^Strain_/) ? "Strain_" : "";
-  my $strain_avail  = ($self->is_strain || $hub->action =~ /^Strain_/) ? "strain_" : "";
+  my $is_strain_view = $hub->action =~ /^Strain_/;
+  my $strain_url    = $is_strain_view ? "Strain_" : "";
+  my $strain_avail  = $is_strain_view ? "strain_" : "";
 
   my $ortho_image = $strain_avail ? 'strain_ortho.gif' : 'compara_ortho.gif';
   my $para_image  = $strain_avail ? 'strain_para.gif' : 'compara_para.gif';
@@ -49,7 +50,7 @@ sub content {
     { title => 'Families',           img => '80/compara_fam.gif',   url => $availability->{'family'}         ? $hub->url({ action => 'Family'             }) : '' },
   ];
 
-  @$buttons  = grep { $_->{title} !~ /^Families$|^Genomic alignments$/ } @$buttons if($self->is_strain); #remove the one we dont show for strains species
+  @$buttons  = grep { $_->{title} !~ /^Families$|^Genomic alignments$/ } @$buttons if($is_strain_view); #remove the one we dont show for strain views
   my $html  = $self->button_portal($buttons, 'portal-small');
      $html .= qq{<p>More views of comparative genomics data, such as multiple alignments and synteny, are available on the <a href="$location">Location</a> page for this gene.</p>};
 

modules/EnsEMBL/Web/Component/Gene/HomologAlignment.pm

@@ -85,10 +85,13 @@ sub content {
         my $label             = $external_species ? $pan_lookup->{$prodname}{'display_name'} : $species_defs->species_label($member_species);
         my $location       = sprintf '%s:%d-%d', $gene->dnafrag->name, $gene->dnafrag_start, $gene->dnafrag_end;
 
-        if (!$second_gene && $member_species ne $species && $hub->param('species_' .$prodname) eq 'off') {
-          $flag = 0;
-          $skipped{$label}++;
-          next;
+        if (!$second_gene && $member_species ne $species) {
+          my $species_toggle = $hub->param('species_' .$prodname);
+          if (!defined $species_toggle || $species_toggle eq 'off') {
+            $skipped{$label}++ if defined $species_toggle;
+            $flag = 0;
+            next;
+          }
         }
 
         if ($gene->stable_id eq $gene_id) {

modules/EnsEMBL/Web/ConfigPacker.pm

@@ -1387,11 +1387,30 @@ sub _summarise_compara_db {
   $sth->execute;
 
   while (my ($sp, $clusterset_id, $strain_type) = $sth->fetchrow_array) {
+    $self->db_tree->{$db_name}{'CLUSTERSET_PRODNAMES'}{$clusterset_id}{$sp} = 1;
     next if exists $preferred_clusterset_id{$sp} && $clusterset_id ne $preferred_clusterset_id{$sp};
     $self->db_tree->{$db_name}{'CLUSTERSETS'}{$sp} = $clusterset_id;
     $self->db_tree->{$db_name}{'STRAIN_TYPES'}{$sp} = $strain_type;
   }
 
+  if (exists $self->db_tree->{$db_name}{'CLUSTERSET_PRODNAMES'}) {
+
+    my $default_oset_spp_aref = $dbh->selectcol_arrayref('
+      select distinct gd.name
+      from method_link_species_set mlss
+        join method_link ml using(method_link_id)
+        join species_set ss using(species_set_id)
+        join species_set_header ssh using(species_set_id)
+        join genome_db gd using(genome_db_id)
+      where ml.type in ("PROTEIN_TREES", "NC_TREES")
+        and trim(leading "collection-" from ssh.name) = "default";
+    ');
+
+    foreach my $sp (@$default_oset_spp_aref) {
+      $self->db_tree->{$db_name}{'CLUSTERSET_PRODNAMES'}{'default'}{$sp} = 1;
+    }
+  }
+
   ###################################################################
   ## Cache MLSS for quick lookup in ImageConfig