From fb42bfa793dbe3f13d770342a5fe48f3289859a2 Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Tue, 21 Oct 2014 12:58:22 +0100
Subject: [PATCH] Make the method 'get_all_somatic_VariationFeatures' works the
same way as 'get_all_VariationFeatures'
---
modules/Bio/EnsEMBL/Slice.pm | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index cae6d53129..5137e4d8cf 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1831,7 +1831,19 @@ sub get_all_VariationFeatures{
=head2 get_all_somatic_VariationFeatures
- Arg [1] : (optional) string $dbtype
+ Args [1] : (optional) ArrayRef $so_terms
+ SequenceOntology terms to limit the fetch to
+ Args [2] : (optional) boolean $without_children
+ Do not query using the children of the given SO terms
+ i.e. query using the given terms directly
+ Args [3] : (optional) ArrayRef $included_so
+ ArrayRef of SequenceOntology which should be queried for
+ without children. This argument allows you to combine SO terms with children
+ from argument 1 with extra non-child SO terms. e.g. you wish to query for
+ all protein_altering_variant (specified in argument 1) variations which
+ would be defined by child SO terms but also wanted stop_retained_variant linked variations
+ defined by this argument
+ Args [4] : (optional) string $dbtype
The dbtype of variation to obtain (i.e. can be different from the "variation" type).
This assumes that the extra db has been added to the DBAdaptor under this name (using the
DBConnection::add_db_adaptor method).
@@ -1844,9 +1856,9 @@ sub get_all_VariationFeatures{
=cut
sub get_all_somatic_VariationFeatures {
- my ($self, $dbtype) = @_;
+ my ($self, $so_terms, $without_children, $included_so, $dbtype) = @_;
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) {
- return $vf_adaptor->fetch_all_somatic_by_Slice($self);
+ return $vf_adaptor->fetch_all_somatic_by_Slice_SO_terms($self, $so_terms, $without_children, $included_so);
}
return [];
}
--
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