diff dir_plugins/HGVSReferenceBase.pm @ 0:e545d0a25ffe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/HGVSReferenceBase.pm	Mon Jul 15 05:17:17 2019 -0400
@@ -0,0 +1,78 @@
+=head1 LICENSE
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2018] EMBL-European Bioinformatics Institute
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+     http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=head1 CONTACT
+
+ Ensembl <http://www.ensembl.org/info/about/contact/index.html>
+    
+=cut
+
+=head1 NAME
+
+  HGVSReferenceBase
+
+=head1 SYNOPSIS
+
+  mv HGVSReferenceBase.pm ~/.vep/Plugins
+  ./vep -i variations.vcf --cache --hgvs --plugin HGVSReferenceBase
+
+=head1 DESCRIPTION
+
+  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
+  reports the reference base for the variant, as used in the longer form.
+  of HGVS. To be used with --hgvs option.
+
+=cut
+
+
+package HGVSReferenceBase;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+use Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor;
+use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Variation::TranscriptVariationAllele;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+
+sub feature_types {
+  return ['Transcript'];
+}
+
+sub variant_feature_types {
+  return ['VariationFeature'];
+}
+
+sub get_header_info {
+  my $self = shift;
+  
+  return {
+    'HGVS_ref' => 'Reference base as may be reported in HGVS transcript level notation',
+  };
+}
+
+sub run {
+  my ($self, $tva) = @_;
+
+  # check var class, this is only useful for  deletions 
+  # or duplications -  a subset of insertions
+  return {} unless $tva->variation_feature->var_class() =~ /del|ins/;
+
+  return $tva->hgvs_transcript_reference() ? {'HGVS_ref' => $tva->hgvs_transcript_reference()} : {};
+
+}
+
+1;