add LoFtool plugin and scores file

LoFtool.pm

@@ -0,0 +1,103 @@
+=head1 LICENSE
+                                                                                                                     
+ Copyright (c) 1999-2015 The European Bioinformatics Institute and
+ Genome Research Limited.  All rights reserved.                                                                      
+                                                                                                                     
+ This software is distributed under a modified Apache license.                                                       
+ For license details, please see
+
+   http://www.ensembl.org/info/about/code_licence.html                                                               
+                                                                                                                     
+=head1 CONTACT                                                                                                       
+
+ William McLaren <wm2@ebi.ac.uk>
+    
+=cut
+
+=head1 NAME
+
+ UpDownDistance
+
+=head1 SYNOPSIS
+
+ mv LoFtool.pm ~/.vep/Plugins
+ mv LoFtool_scores.txt ~/.vep/Plugins
+ perl variant_effect_predictor.pl -i variants.vcf --plugin LoFtool
+
+=head1 DESCRIPTION
+
+ Add LoFtool scores to the VEP output.
+ 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.
+
+ perl variant_effect_predictor.pl -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 $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;
+