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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/TSSDistance.pm	Mon Jul 15 05:20:39 2019 -0400
@@ -0,0 +1,85 @@
+=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
+
+ TSSDistance
+
+=head1 SYNOPSIS
+
+ mv TSSDistance.pm ~/.vep/Plugins
+ ./vep -i variations.vcf --plugin CCDSFilter
+
+=head1 DESCRIPTION
+
+ A VEP plugin that calculates the distance from the transcription
+ start site for upstream variants.
+
+=cut
+
+package TSSDistance;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub get_header_info {
+    return {
+        TSSDistance => "Distance from the transcription start site"
+    };
+}
+
+sub feature_types {
+    return ['Transcript'];
+}
+
+sub variant_feature_types {
+    return ['BaseVariationFeature'];
+}
+
+sub run {
+    my ($self, $tva) = @_;
+
+    my $t = $tva->transcript;
+    my $vf = $tva->base_variation_feature;
+
+    my $dist;
+
+    if ($t->strand == 1) {
+        $dist = $t->start - $vf->end;
+    }
+    else {
+        $dist = $vf->start - $t->end;
+    }
+
+    if ($dist > 0) {
+        return {
+            TSSDistance => $dist,
+        }
+    }
+    else {
+        return {};
+    }
+}
+
+1;