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Update NearestExonJB #771

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Update NearestExonJB #771

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c52bf0f
Include intronic variants
dglemos Jan 30, 2025
9a1e21b
Change output
dglemos Jan 30, 2025
d38079f
Apply to intron variants
dglemos Jan 31, 2025
a38e408
Update plugin description
dglemos Jan 31, 2025
baa5275
Format output to be the same as default
dglemos Feb 13, 2025
ee4e683
Update description
dglemos Feb 13, 2025
819b1a9
Remove comment
dglemos Feb 13, 2025
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75 changes: 69 additions & 6 deletions NearestExonJB.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ limitations under the License.

This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
finds the nearest exon junction boundary to a coding sequence variant. More than
one boundary may be reported if the boundaries are equidistant.
one boundary may be reported if the boundaries are equidistant or if using option
--intronic.

The plugin will report the Ensembl identifier of the exon, the distance to the
exon boundary, the boundary type (start or end of exon) and the total
Expand All @@ -44,9 +45,16 @@ limitations under the License.

max_range : maximum search range in bp (default: 10000)

intronic : set to 1 to check nearest exons for intronic variants (default: 0)
returns the nearest exon upstream and downstream without considering
the max_range.


Parameters are passed e.g.:

--plugin NearestExonJB,max_range=50000
--plugin NearestExonJB,max_range=50000,intronic=1
--plugin NearestExonJB,intronic=1

=cut

Expand All @@ -63,6 +71,7 @@ my $char_sep = "|";

my %CONFIG = (
max_range => 10000,
intronic => 0
);

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Suggesting we change the get_header_info since we support intron_variants now

sub new {
Expand Down Expand Up @@ -106,9 +115,39 @@ sub run {
my $loc_string = sprintf("%s:%s-%i-%i", $trv->transcript_stable_id, $vf->{chr} || $vf->seq_region_name, $vf->{start}, $vf->{end});

if(!exists($self->{_cache}) || !exists($self->{_cache}->{$loc_string})) {
my $exons = $trv->_overlapped_exons;
my $exons = $trv->_overlapped_exons; # intronic variants do not overlap any exon
my %dists;
my $min = $CONFIG{max_range};

# For option --intronic, fetch the list of exons with different method
# Do not take into account the max_range
if(scalar @{$exons} == 0 && $CONFIG{intronic} == 1) {
my $intron_numbers = $trv->intron_number();
my $consequences = join(",", map { $_->SO_term } @{$tva->get_all_OverlapConsequences});

if(defined $intron_numbers && $consequences =~ /intron/) {
$exons = $trv->_sorted_exons;
my ($intron_number, $total_number) = split(/\//, $intron_numbers);

# Get the number of exons before and after the intron
my $exon_before = $intron_number;
my $exon_after = $intron_number + 1;

my @exons_tmp;
# Reverse strand we get the exons from the end of the list
if($tva->transcript->strand < 0) {
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Suggesting that we just directly modify the $exons like this

if ($tva->transcript->strand < 0) {
@$exons = ($exons->[-$intron_number], $exons->[-($intron_number + 1)]);
}
else {
@$exons = ($exons->[$intron_number - 1], $exons->[$intron_number]);  
}

push(@exons_tmp, $exons->[-$exon_before]);
push(@exons_tmp, $exons->[-$exon_after]);
}
else {
push(@exons_tmp, $exons->[$exon_before -1]);
push(@exons_tmp, $exons->[$exon_after -1]);
}

$exons = \@exons_tmp;
}
}

foreach my $exon (@$exons) {
my $startD = abs ($vf->start - $exon->seq_region_start);
my $endD = abs ($vf->end - $exon->seq_region_end);
Expand All @@ -128,9 +167,34 @@ sub run {
}

my @finalRes;
foreach my $exon (keys %dists){
if (exists $dists{$exon}{$min}) {
push(@finalRes, $exon.$char_sep.$min.$char_sep.$dists{$exon}{$min}.$char_sep.$dists{$exon}{len})
# For option --intronic, return the closest exons (upstream/dowsntream) from the intron
if(scalar @{$exons} == 2 && $CONFIG{intronic} == 1) {
foreach my $exon (keys %dists) {
my $inner_hash = $dists{$exon};
my $length_value;
my $type;
my $distance_value;

for my $internal_key (keys %{$inner_hash}) {
if($internal_key eq "len") {
$length_value = $inner_hash->{$internal_key};
}
else {
$type = $inner_hash->{$internal_key};
$distance_value = $internal_key;
}
}

my $string = $exon . $char_sep . $distance_value . $char_sep . $type . $char_sep . $length_value;
push(@finalRes, $string);
}
}
else {
# This is the default behaviour of the plugin
foreach my $exon (keys %dists){
if (exists $dists{$exon}{$min}) {
push(@finalRes, $exon.$char_sep.$min.$char_sep.$dists{$exon}{$min}.$char_sep.$dists{$exon}{len})
}
}
}

Expand All @@ -140,4 +204,3 @@ sub run {
}

1;