diff dir_plugins/GO.pm @ 3:49397129aec0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/GO.pm	Mon Jul 15 05:20:39 2019 -0400
@@ -0,0 +1,102 @@
+=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
+
+ GO
+
+=head1 SYNOPSIS
+
+ mv GO.pm ~/.vep/Plugins
+ ./vep -i variations.vcf --plugin GO
+
+=head1 DESCRIPTION
+
+ A VEP plugin that retrieves Gene Ontology terms associated with
+ transcripts/translations via the Ensembl API. Requires database connection.
+ 
+=cut
+
+package GO;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub new {
+  my $class = shift;
+  
+  my $self = $class->SUPER::new(@_);
+  
+  # connect to DB for offline users
+  my $config = $self->{config};
+  my $reg = $config->{reg};
+  
+  if(!defined($self->{config}->{sa})) {
+    $reg = 'Bio::EnsEMBL::Registry';
+    $reg->load_registry_from_db(
+      -host       => $config->{host},
+      -user       => $config->{user},
+      -pass       => $config->{password},
+      -port       => $config->{port},
+      -db_version => $config->{db_version},
+      -species    => $config->{species} =~ /^[a-z]+\_[a-z]+/i ? $config->{species} : undef,
+      -verbose    => $config->{verbose},
+      -no_cache   => $config->{no_slice_cache},
+    );
+  }
+  
+  return $self;
+}
+
+sub version {
+  return 73;
+}
+
+sub feature_types {
+  return ['Transcript'];
+}
+
+sub get_header_info {
+  return { 'GO' => 'GO terms associated with protein product'};
+}
+
+sub run {
+  my ($self, $tva) = @_;
+  
+  my $tr = $tva->transcript->translation;
+  return {} unless defined($tr);
+  
+  my $entries = $tr->get_all_DBEntries('GO');
+  
+  my $string = join(",", map {$_->display_id.':'.$_->description} @$entries);
+  $string =~ s/\s+/\_/g;
+  
+  return { GO => $string };
+}
+
+1;
+