Skip to content

Access more homology metadata via multi packed file #1168

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
twalsh-ebi wants to merge 1 commit into
base: postreleasefix/116
Choose a base branch
from
Open

Access more homology metadata via multi packed file #1168

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
65 changes: 65 additions & 0 deletions modules/EnsEMBL/Web/ConfigPacker.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1207,6 +1207,69 @@ sub _build_compara_mlss {
$dest->{'MLSS_IDS'} = \%mlss;
}

sub _build_gene_tree_stats_mlss {
my ($self,$dbh,$dest) = @_;

# Take the default gene-tree collection, if available.
# Otherwise, take the largest gene-tree collection.
my $sql = q(
select method_link_species_set_id
from method_link_species_set mlss
join method_link ml
using (method_link_id)
join species_set_header ssh
using (species_set_id)
where ml.type = ?
order by field(ssh.name, "collection-default", "default") desc, ssh.size desc
limit 1
);

my %gene_tree_stats_mlss_ids;
foreach my $method_type ('PROTEIN_TREES', 'NC_TREES') {
my ($row) = $dbh->selectrow_arrayref($sql, undef, $method_type);
if ($row) {
$gene_tree_stats_mlss_ids{$method_type} = $row->[0];
}
}

$dest->{'GENE_TREE_STATS_MLSS_IDS'} = \%gene_tree_stats_mlss_ids;
}

sub _build_homology_mlss_tags {
my ($self,$dbh,$dest) = @_;

# Homology MLSS tags may be stored in the method_link_species_set_attr
# or method_link_species_set_tag tables. It just so happens that all
# the tags we are currently interested in are to be found in the
# method_link_species_set_attr table.
my $sth = $dbh->prepare(q(
select method_link_species_set_id,
goc_quality_threshold,
wga_quality_threshold
from method_link_species_set
join method_link
using (method_link_id)
join method_link_species_set_attr
using (method_link_species_set_id)
where goc_quality_threshold is not null
or wga_quality_threshold is not null
));
$sth->execute;
my %hom_mlss_tags;
while (my ($mlss_id, $goc_threshold, $wga_threshold) = $sth->fetchrow_array) {
$hom_mlss_tags{$mlss_id} = {};

if (defined $goc_threshold) {
$hom_mlss_tags{$mlss_id}{goc_quality_threshold} = $goc_threshold;
}

if (defined $wga_threshold) {
$hom_mlss_tags{$mlss_id}{wga_quality_threshold} = $wga_threshold;
}
}
$dest->{'HOMOLOGY_MLSS_TAGS'} = \%hom_mlss_tags;
}

sub _summarise_compara_db {
my ($self, $code, $db_name) = @_;

Expand Down Expand Up @@ -1412,6 +1475,8 @@ sub _summarise_compara_db {

$self->_build_compara_default_aligns($dbh,$self->db_tree->{$db_name});
$self->_build_compara_mlss($dbh,$self->db_tree->{$db_name});
$self->_build_gene_tree_stats_mlss($dbh,$self->db_tree->{$db_name});
$self->_build_homology_mlss_tags($dbh,$self->db_tree->{$db_name});

##
###################################################################
Expand Down
34 changes: 23 additions & 11 deletions modules/EnsEMBL/Web/Document/HTML/Compara/GeneTrees.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,17 +49,29 @@ sub format_gene_tree_stats {
my $page = $self->hub->param('page');
return unless $compara_db;

my $mlss_adaptor = $compara_db->get_adaptor('MethodLinkSpeciesSet');
my $all_mlsss = $mlss_adaptor->fetch_all_by_method_link_type($method);
# Give preference to default gene-tree collection(s), if available.
my @default_mlsss = grep { $_->species_set->name =~ /^(collection-)?default$/ } @$all_mlsss;
$all_mlsss = \@default_mlsss if (@default_mlsss);
# Take the largest relevant gene-tree collection.
my ($mlss) = sort {$b->species_set->size <=> $a->species_set->size} @$all_mlsss;
return unless $mlss;

my $species_tree_adaptor = $compara_db->get_adaptor('SpeciesTree');
my $species_tree = $mlss->species_tree;
my $species_tree;
my $mlss_ids_by_method_type = $self->hub->species_defs->multi_hash->{'DATABASE_COMPARA'}{'GENE_TREE_STATS_MLSS_IDS'} || {};
if (exists $mlss_ids_by_method_type->{$method} && $mlss_ids_by_method_type->{$method}) {
# If a pre-selected gene-tree collection is available,
# we get that gene-tree collection's species tree.
my $mlss_id = $mlss_ids_by_method_type->{$method};
my $species_tree_adaptor = $compara_db->get_adaptor('SpeciesTree');
# We fetch the 'default' species tree of the gene-tree collection, as
# opposed to other kinds of gene tree (e.g. 'cafe', 'full_species_tree').
$species_tree = $species_tree_adaptor->fetch_by_method_link_species_set_id_label($mlss_id, 'default');
} else {
# If a gene-tree collection has not been pre-selected, select it now.
my $mlss_adaptor = $compara_db->get_adaptor('MethodLinkSpeciesSet');
my $all_mlsss = $mlss_adaptor->fetch_all_by_method_link_type($method);
# Give preference to default gene-tree collection(s), if available.
my @default_mlsss = grep { $_->species_set->name =~ /^(collection-)?default$/ } @$all_mlsss;
$all_mlsss = \@default_mlsss if (@default_mlsss);
# Take the largest relevant gene-tree collection.
my ($mlss) = sort {$b->species_set->size <=> $a->species_set->size} @$all_mlsss;
$species_tree = $mlss->species_tree if $mlss;
}

return unless $species_tree;

# Reads the species set that are defined in the database (if any)
my $ordered_species = $hub->order_species_by_clade($species_tree->root->get_all_leaves);
Expand Down
19 changes: 17 additions & 2 deletions modules/EnsEMBL/Web/Object/Gene.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -821,15 +821,21 @@ sub fetch_homology_species_hash {
my $homology_description = shift;
my $compara_db = shift || 'compara';
my $name_lookup = {};
my $db_key;
if ($compara_db =~ /pan/) {
my $pan_info = $self->hub->species_defs->multi_val('PAN_COMPARA_LOOKUP');
foreach (keys %$pan_info) {
$name_lookup->{$_} = $pan_info->{$_}{'species_url'};
}
$db_key = 'DATABASE_COMPARA_PAN_ENSEMBL';
}
else {
$name_lookup = $self->hub->species_defs->prodnames_to_urls_lookup;
$db_key = 'DATABASE_COMPARA';
}

my $hom_mlss_tags = $self->hub->species_defs->multi_hash->{$db_key}->{'HOMOLOGY_MLSS_TAGS'} // {};

my ($homologies, $classification, $query_member) = $self->get_homologies($homology_source, $homology_description, $compara_db);
my %homologues;

Expand All @@ -847,9 +853,18 @@ sub fetch_homology_species_hash {
$target_member = $gene_member;
$dnds_ratio = $homology->dnds_ratio;
$goc_score = $homology->goc_score;
$goc_threshold = $homology->method_link_species_set->get_value_for_tag('goc_quality_threshold');

my $mlss_id = $homology->method_link_species_set_id;
if (exists $hom_mlss_tags->{$mlss_id} && exists $hom_mlss_tags->{$mlss_id}{'goc_quality_threshold'}) {
$goc_threshold = $hom_mlss_tags->{$mlss_id}{'goc_quality_threshold'};
}

$wgac = $homology->wga_coverage;
$wga_threshold = $homology->method_link_species_set->get_value_for_tag('wga_quality_threshold');

if (exists $hom_mlss_tags->{$mlss_id} && exists $hom_mlss_tags->{$mlss_id}{'wga_quality_threshold'}) {
$wga_threshold = $hom_mlss_tags->{$mlss_id}{'wga_quality_threshold'};
}

$highconfidence = $homology->is_high_confidence;
}
}
Expand Down