Add plugin for pLI on ExAC data

ExACpLI.pm

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+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2017] 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
+
+ Please email comments or questions to the public Ensembl
+ developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <http://www.ensembl.org/Help/Contact>.
+
+=cut
+
+=head1 NAME
+
+ExACpLI - Add ExAC pLI to the VEP output 
+
+=head1 SYNOPSIS
+
+  mv ExACpLI.pm ~/.vep/Plugins
+  mv ExACpLI_values.txt ~/.vep/Plugins
+  perl vep.pl -i variants.vcf --plugin ExACpLI
+
+=head1 DESCRIPTION
+
+
+  A VEP plugin that adds the probabililty of being loss-of-function 
+  intolerant (pLI) to the VEP output.
+  
+  Lek et al. (2016) estimated pLI using the expectation-maximization 
+  (EM) algorithm and data from 60,706 individuals from 
+  ExAC (http://exac.broadinstitute.org/about). The closer pLI is to 1, 
+  the more likely the transcript is loss-of-function (LoF) intolerant.
+
+  The data for the plugin is provided by Kaitlin Samocha and Daniel MacArthur. 
+  See https://www.ncbi.nlm.nih.gov/pubmed/27535533 for a description 
+  of the dataset and analysis.
+
+  The ExACpLI_values.txt file is found alongside the plugin in the 
+  VEP_plugins GitHub repository. The file contains the fields gene and pLI 
+  extracted from the file at 
+    
+    ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint/
+      fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
+
+  To use another values file, add it as a parameter i.e.
+
+     perl vep.pl -i variants.vcf --plugin ExACpLI,values_file.txt
+
+
+=cut
+
+package ExACpLI;
+
+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{'ExACpLI.pm'};
+    $plugin_dir =~ s/ExACpLI\.pm//i;
+    $file = $plugin_dir.'/ExACpLI_values.txt';
+  }
+
+  die("ERROR: ExACpLI values file $file not found\n") unless $file && -e $file;
+
+  open my $fh, "<",  $file;
+  my %scores;
+
+  while(<$fh>) {
+    chomp;
+    my ($gene, $score) = split;
+    next if $score eq 'pLI';
+    $scores{lc($gene)} = sprintf("%.2f", $score);
+  }
+
+  close $fh;
+
+  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 {
+    ExACpLI => "ExACpLI value 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)} ? { ExACpLI => $self->{scores}->{lc($symbol)}} : {};
+}
+
+1;
+