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Generalise tandem_duplication as tandem_repeat #1057

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Dec 14, 2023
Merged

Generalise tandem_duplication as tandem_repeat #1057

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6 changes: 3 additions & 3 deletions modules/Bio/EnsEMBL/Variation/BaseVariationFeatureOverlapAllele.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -422,15 +422,15 @@ sub _bvf_preds {
my $support_vars = $bvf->structural_variation->get_all_SupportingStructuralVariants;
my @support_terms = map { $_->class_SO_term } @{$support_vars};

$is_CNV_deletion = grep(/deletion|loss/i, @support_terms);
$is_CNV_insertion = grep(/insertion|duplication|gain/i, @support_terms);
$is_CNV_deletion = grep(/deletion|loss/i, @support_terms);
$is_CNV_insertion = grep(/insertion|duplication|gain|tandem/i, @support_terms);
}

if($class_SO_term =~ /deletion|loss/i || $is_CNV_deletion) {
$self->_update_preds($bvf_preds, 'deletion', 1, \$pred_digest);
$self->_update_preds($bvf_preds, 'decrease_length', 1, \$pred_digest);
}
elsif($class_SO_term =~ /insertion|duplication|gain/i || $is_CNV_insertion) {
elsif($class_SO_term =~ /insertion|duplication|gain|tandem/i || $is_CNV_insertion) {
$self->_update_preds($bvf_preds, 'insertion', 1, \$pred_digest);
$self->_update_preds($bvf_preds, 'increase_length', 1, \$pred_digest);
}
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11 changes: 6 additions & 5 deletions modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ sub copy_number_gain {

return (
duplication(@_) or
tandem_duplication(@_) or
tandem_repeat(@_) or
$bvf->class_SO_term(undef, 1) =~ /gain/i or
grep(/gain/i, _supporting_cnv_terms($bvf))
);
Expand All @@ -269,11 +269,11 @@ sub duplication {
($bvf->class_SO_term(undef, 1) =~ /duplication/i) or
grep(/duplication/i, _supporting_cnv_terms($bvf))
) and
(not tandem_duplication(@_))
(not tandem_repeat(@_))
);
}

sub tandem_duplication {
sub tandem_repeat {
my ($bvfoa, $feat, $bvfo, $bvf) = @_;
$bvf ||= $bvfoa->base_variation_feature;

Expand All @@ -295,8 +295,9 @@ sub tandem_duplication {
if($bvf->isa('Bio::EnsEMBL::Variation::StructuralVariationFeature')) {
return (
($bvf->class_SO_term(undef, 1) eq 'tandem_duplication') or
($bvf->class_SO_term(undef, 1) =~ /tandem_duplication/i) or
grep(/tandem_duplication/i, _supporting_cnv_terms($bvf))
($bvf->class_SO_term(undef, 1) eq 'tandem_repeat') or
($bvf->class_SO_term(undef, 1) =~ /tandem/i) or
grep(/tandem/i, _supporting_cnv_terms($bvf))
);
}
}
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