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Thread unique synteny regions along main chromosome #1130

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f662e4c
Thread unique synteny regions along main chromosome
twalsh-ebi Dec 16, 2025
b4c35dd
Update info panel for chromosomes lacking synteny regions
twalsh-ebi Dec 16, 2025
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60 changes: 48 additions & 12 deletions modules/EnsEMBL/Draw/GlyphSet/Vsynteny.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -101,19 +101,55 @@ sub _init {
my $highlights_main = { $chr => [] };
my $CANSEE_OTHER = $config->{'other_species_installed'};

# When working with a synteny dataset such as the Hsap synteny, we need to be able to distinguish
# between the main and other synteny regions, even if both are from the same genome. Moreover, we
# may encounter synteny pairs between two regions on the same chromosome in the same genome. In
# such cases, the Compara API may return the same synteny pair twice, without distinction between
# the two syntenic regions. To help make sense of all this, we generate a synteny region key for
# each region of the main chromosome that is in a synteny pair, so that we can then sort the
# synteny regions in order to 'thread' them along the main chromosome.
my %syntenies_by_main_region;
foreach my $synteny_region (@$synteny_data) {
my ($main_dfr, $other_dfr);
my ($dfr1, $dfr2) = @{$synteny_region->get_all_DnaFragRegions};

foreach my $dfr (@{$synteny_region->get_all_DnaFragRegions}) {
if (lc($self_production_name) eq lc($dfr->dnafrag->genome_db->name) and $dfr->dnafrag->genome_db->name eq $other_production_name) {
$main_dfr = $dfr;
$other_dfr = $dfr;
} elsif ($dfr->dnafrag->genome_db->name eq $other_production_name) {
$other_dfr = $dfr;
} else {
$main_dfr = $dfr;
}
if (lc($dfr1->dnafrag->genome_db->name) eq lc($self_production_name) && $dfr1->dnafrag->name eq $chr) {

my $dfr1_synteny_region_key = join(
':',
$synteny_region->dbID,
$dfr1->dnafrag->dbID,
$dfr1->dnafrag_start,
$dfr1->dnafrag_end,
$dfr1->dnafrag_strand,
);

$syntenies_by_main_region{$dfr1_synteny_region_key} = [$dfr1_synteny_region_key, $dfr1, $dfr2];
}

if (lc($dfr2->dnafrag->genome_db->name) eq lc($self_production_name) && $dfr2->dnafrag->name eq $chr) {

my $dfr2_synteny_region_key = join(
':',
$synteny_region->dbID,
$dfr2->dnafrag->dbID,
$dfr2->dnafrag_start,
$dfr2->dnafrag_end,
$dfr2->dnafrag_strand,
);

$syntenies_by_main_region{$dfr2_synteny_region_key} = [$dfr2_synteny_region_key, $dfr2, $dfr1];
}
}

my @synteny_regions = sort {
$a->[1]->dnafrag_start <=> $b->[1]->dnafrag_start
|| $b->[1]->dnafrag_end <=> $a->[1]->dnafrag_end
|| $b->[1]->dnafrag_strand <=> $a->[1]->dnafrag_strand
|| $a->[0] cmp $b->[0]
} values %syntenies_by_main_region;

foreach my $synteny_region (@synteny_regions) {
my ($synteny_region_key, $main_dfr, $other_dfr) = @$synteny_region;

my $other_chr = $other_dfr->dnafrag->name;

Expand Down Expand Up @@ -148,7 +184,7 @@ sub _init {
});

push @{$highlights_main->{$chr}}, {
'id' => $synteny_region->dbID,
'id' => $synteny_region_key,
'start' => $main_dfr->dnafrag_start,
'end' => $main_dfr->dnafrag_end,
'col' => $COL,
Expand All @@ -173,7 +209,7 @@ sub _init {

push @{$highlights_secondary->{$other_chr}}, {
'rel_ori' => $main_dfr->dnafrag_strand * $other_dfr->dnafrag_strand,
'id' => $synteny_region->dbID,
'id' => $synteny_region_key,
'start' => $other_dfr->dnafrag_start,
'end' => $other_dfr->dnafrag_end,
'col' => $COL,
Expand Down
27 changes: 12 additions & 15 deletions modules/EnsEMBL/Web/Component/Location/SyntenyImage.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -37,38 +37,35 @@ sub content {
my $hub = $self->hub;
my $object = $self->object || $self->hub->core_object('location');
my $species = $hub->species;
my $this_prodname = $hub->species_defs->get_config($species, 'SPECIES_PRODUCTION_NAME');
my %synteny = $hub->species_defs->multi('DATABASE_COMPARA', 'SYNTENY');
my $other = $self->hub->otherspecies;
my $other_prodname = $hub->species_defs->get_config($other, 'SPECIES_PRODUCTION_NAME');
my $chr = $object->seq_region_name;
my %chr_1 = map { $_, 1 } @{$hub->species_defs->ENSEMBL_CHROMOSOMES || []};
my %chr_2 = map { $_, 1 } @{$hub->species_defs->get_config($other, 'ENSEMBL_CHROMOSOMES') || []};

unless ($synteny{$other_prodname}) {
unless ($synteny{$this_prodname}{$other_prodname}) {
$hub->problem('fatal', "Can't display synteny", "There is no synteny data for these two species ($species and $other)");
return undef;
}

my $ka = $hub->get_adaptor('get_KaryotypeBandAdaptor', 'core', $species);
my $ka2 = $hub->get_adaptor('get_KaryotypeBandAdaptor', 'core', $other);
my $compara_db = $hub->database('compara');
my $raw_data = $object->chromosome->get_all_compara_Syntenies($other, undef, $compara_db);
my $chr_length = $object->chromosome->length;
my $other_chr;

OUTER:
foreach my $synteny_region (@$raw_data) {
foreach my $dfr (@{$synteny_region->get_all_DnaFragRegions}) {
# Check if any of the synteny regions map to a chromosome in the other species
if ($dfr->dnafrag->genome_db->name eq $other_prodname && $chr_2{$dfr->dnafrag->name}) {
$other_chr = 1;
last OUTER;
}
}

my $genome_dba = $compara_db->get_GenomeDBAdaptor();
my @synteny_gdbs = ($genome_dba->fetch_by_name_assembly($this_prodname));
if ($other_prodname ne $this_prodname) {
push(@synteny_gdbs, $genome_dba->fetch_by_name_assembly($other_prodname));
}

my $mlss = $compara_db->get_MethodLinkSpeciesSetAdaptor->fetch_by_method_link_type_GenomeDBs('SYNTENY', \@synteny_gdbs);
my $raw_data = $compara_db->get_SyntenyRegionAdaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $object->chromosome);

my $image_html;
if ($chr_1{$chr} && $other_chr) {
if (scalar(@$raw_data) > 0) {

my ($localgenes, $offset) = $object->get_synteny_local_genes;
my $loc = (@$localgenes ? $localgenes->[0]->start + $object->seq_region_start : 1); # Jump loc to the location of the genes
Expand Down Expand Up @@ -102,7 +99,7 @@ sub content {
$image_html = $image->render;
}
else {
$image_html = $self->info_panel("Unassembled chromosomes", "<p>No image can be drawn, because the syntenous species has no assembled chromosomes.</p>");
$image_html = $self->info_panel("Unavailable synteny regions", "<p>No image can be drawn, because this chromosome lacks synteny regions with the selected species.</p>");
}
my $chr_form = $self->chromosome_form('Vsynteny');

Expand Down