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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/LoFtool.pm	Mon Jul 15 05:20:39 2019 -0400
@@ -0,0 +1,122 @@
+=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
+
+ LoFtool
+
+=head1 SYNOPSIS
+
+  mv LoFtool.pm ~/.vep/Plugins
+  mv LoFtool_scores.txt ~/.vep/Plugins
+  ./vep -i variants.vcf --plugin LoFtool
+
+=head1 DESCRIPTION
+
+  Add LoFtool scores to the VEP output.
+
+  LoFtool provides a rank of genic intolerance and consequent
+  susceptibility to disease based on the ratio of Loss-of-function (LoF)
+  to synonymous mutations for each gene in 60,706 individuals from ExAC,
+  adjusting for the gene de novo mutation rate and evolutionary protein
+  conservation. The lower the LoFtool gene score percentile the most
+  intolerant is the gene to functional variation. For more details please see
+  (Fadista J et al. 2017), PMID:27563026.
+  The authors would like to thank the Exome Aggregation Consortium and
+  the groups that provided exome variant data for comparison. A full
+  list of contributing groups can be found at http://exac.broadinstitute.org/about.
+
+  The LoFtool_scores.txt file is found alongside the plugin in the
+  VEP_plugins GitHub repo.
+
+  To use another scores file, add it as a parameter i.e.
+
+  ./vep -i variants.vcf --plugin LoFtool,scores_file.txt
+
+=cut
+
+package LoFtool;
+
+use strict;
+use warnings;
+
+use DBI;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub new {
+  my $class = shift;
+
+  my $self = $class->SUPER::new(@_);
+  
+  my $file = $self->params->[0];
+
+  if(!$file) {
+    my $plugin_dir = $INC{'LoFtool.pm'};
+    $plugin_dir =~ s/LoFtool\.pm//i;
+    $file = $plugin_dir.'/LoFtool_scores.txt';
+  }
+  
+  die("ERROR: LoFtool scores file $file not found\n") unless $file && -e $file;
+  
+  open IN, $file;
+  my %scores;
+  
+  while(<IN>) {
+    chomp;
+    my ($gene, $score) = split;
+    next if !defined($score) || $score eq 'LoFtool_percentile';
+    $scores{lc($gene)} = sprintf("%g", $score);
+  }
+  
+  close IN;
+  
+  die("ERROR: No scores read from $file\n") unless scalar keys %scores;
+  
+  $self->{scores} = \%scores;
+  
+  return $self;
+}
+
+sub feature_types {
+  return ['Transcript'];
+}
+
+sub get_header_info {
+  return {
+    LoFtool => "LoFtool score for gene"
+  };
+}
+
+sub run {
+  my $self = shift;
+  my $tva = shift;
+  
+  my $symbol = $tva->transcript->{_gene_symbol} || $tva->transcript->{_gene_hgnc};
+  return {} unless $symbol;
+  
+  return $self->{scores}->{lc($symbol)} ? { LoFtool => $self->{scores}->{lc($symbol)}} : {};
+}
+
+1;
+