From ec1aff6e5c03d722324c7d5ae8b87bc93d3154cd Mon Sep 17 00:00:00 2001
From: William McLaren <wm2@ebi.ac.uk>
Date: Wed, 20 Mar 2013 13:51:14 +0000
Subject: [PATCH] changes for PhenotypeFeature API in variation
---
modules/Bio/EnsEMBL/Slice.pm | 68 +++++++++++++++++++++++++++---------
1 file changed, 52 insertions(+), 16 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index e20864779d..b8c528143b 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1849,20 +1849,20 @@ sub get_all_somatic_VariationFeatures_by_source {
}
-=head2 get_all_VariationFeatures_with_annotation
+=head2 get_all_VariationFeatures_with_phenotype
Arg [1] : $variation_feature_source [optional]
- Arg [2] : $annotation_source [optional]
- Arg [3] : $annotation_name [optional]
+ Arg [2] : $phenotype_source [optional]
+ Arg [3] : $phenotype_name [optional]
Description : returns all germline variation features on this slice associated with a phenotype.
This function will only work correctly if the variation database has been
attached to the core database.
If $variation_feature_source is set only variations from that source
are retrieved.
- If $annotation_source is set only variations whose annotations come from
+ If $phenotype_source is set only variations whose annotations come from
$annotation_source will be retrieved.
- If $annotation_name is set only variations with that annotation will be retrieved.
- $annotation_name can be a phenotype's internal dbID.
+ If $phenotype_name is set only variations with that annotation will be retrieved.
+ $phenotype_name can be a phenotype's internal dbID.
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview
@@ -1870,41 +1870,41 @@ sub get_all_somatic_VariationFeatures_by_source {
=cut
-sub get_all_VariationFeatures_with_annotation{
+sub get_all_VariationFeatures_with_phenotype {
my $self = shift;
my $source = shift;
my $p_source = shift;
- my $annotation = shift;
+ my $phenotype = shift;
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor) {
- return $vf_adaptor->fetch_all_with_annotation_by_Slice($self, $source, $p_source, $annotation);
+ return $vf_adaptor->fetch_all_with_phenotype_by_Slice($self, $source, $p_source, $phenotype);
}
else {
return [];
}
}
-=head2 get_all_somatic_VariationFeatures_with_annotation
+=head2 get_all_somatic_VariationFeatures_with_phenotype
Arg [1] : $variation_feature_source [optional]
- Arg [2] : $annotation_source [optional]
- Arg [3] : $annotation_name [optional]
+ Arg [2] : $phenotype_source [optional]
+ Arg [3] : $phenotype_name [optional]
Description : returns all somatic variation features on this slice associated with a phenotype.
- (see get_all_VariationFeatures_with_annotation for further documentation)
+ (see get_all_VariationFeatures_with_phenotype for further documentation)
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Status : Stable
=cut
-sub get_all_somatic_VariationFeatures_with_annotation{
+sub get_all_somatic_VariationFeatures_with_phenotype{
my $self = shift;
my $source = shift;
my $p_source = shift;
- my $annotation = shift;
+ my $phenotype = shift;
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor) {
- return $vf_adaptor->fetch_all_somatic_with_annotation_by_Slice($self, $source, $p_source, $annotation);
+ return $vf_adaptor->fetch_all_somatic_with_phenotype_by_Slice($self, $source, $p_source, $phenotype);
}
else {
return [] unless $vf_adaptor;
@@ -2216,6 +2216,42 @@ sub get_all_VariationFeatures_by_Population {
}
+=head2 get_all_PhenotypeFeatures
+ Args : string $type [optional]
+ Description : Returns all phenotype features on this slice. This function will
+ only work correctly if the variation database has been attached to the core
+ database.
+ If $type is specified, only phenotypes annotated on the given
+ object type will be returned
+ ReturnType : listref of Bio::EnsEMBL::Variation::PhenotypeFeature
+ Exceptions : none
+ Caller : web
+ Status : Stable
+
+=cut
+
+sub get_all_PhenotypeFeatures {
+ my $self = shift;
+ my $type = shift;
+
+ if(!$self->adaptor()) {
+ warning('Cannot get phenotype features without attached adaptor');
+ return undef;
+ }
+
+ my $pf_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
+ -species => $self->adaptor()->db()->species,
+ -type => "PhenotypeFeature"
+ );
+
+ if(defined($type)) {
+ return $pf_adaptor->fetch_all_by_Slice_type($self, $type);
+ }
+ else {
+ return $pf_adaptor->fetch_all_by_Slice($self);
+ }
+}
+
=head2 get_all_IndividualSlice
--
GitLab