diff dir_plugins/LOVD.pm @ 0:e545d0a25ffe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/LOVD.pm	Mon Jul 15 05:17:17 2019 -0400
@@ -0,0 +1,128 @@
+=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
+
+ LOVD
+
+=head1 SYNOPSIS
+
+ mv LOVD.pm ~/.vep/Plugins
+ ./vep -i variations.vcf --plugin LOVD
+
+=head1 DESCRIPTION
+
+ A VEP plugin that retrieves LOVD variation data from http://www.lovd.nl/.
+ 
+ Please be aware that LOVD is a public resource of curated variants, therefore
+ please respect this resource and avoid intensive querying of their databases
+ using this plugin, as it will impact the availability of this resource for
+ others.
+
+=cut
+
+package LOVD;
+
+use strict;
+use warnings;
+use LWP::UserAgent;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub version {
+    return '2.5';
+}
+
+sub feature_types {
+    return ['Transcript'];
+}
+
+sub get_header_info {
+    return {
+        LOVD => "LOVD variant ID",
+    };
+}
+
+sub run {
+    my ($self, $tva) = @_;
+    
+    $self->{has_cache} = 1;
+
+    my %hg_assembly = ( 'grch37' => 'hg19', 'grch38' => 'hg38' );
+    my $assembly = lc($self->{config}->{assembly});
+
+    # only works on human
+    die("ERROR: LOVD plugin works only on human data") unless $self->{config}->{species} =~ /human|homo/i;
+    
+    # only work on 2 human assemblies
+    die("ERROR: LOVD plugin works only on human assemblies ".join(' and ', keys(%hg_assembly))) unless $hg_assembly{$assembly};
+
+    # get the VF object
+    my $vf = $tva->variation_feature;
+    return {} unless defined $vf;
+    
+    # set up a LWP UserAgent
+    my $ua = LWP::UserAgent->new;
+    $ua->env_proxy;
+
+    my $chr = $vf->{chr};
+    $chr =~ s/^chr//;
+    
+    my $locus = sprintf('chr%s:%s_%s', $chr, $vf->{start}, $vf->{end});
+    
+    my $data;
+    
+    # check the cache
+    if(!exists($self->{lovd_cache}->{$locus})) {
+        
+        # construct a LOVD URL
+        my $url = sprintf('http://www.lovd.nl/search.php?build=%s&position=%s', $hg_assembly{$assembly}, $locus);
+        
+        # get the accession (only need the head to get the redirect URL that contains the accession)
+        my $response = $ua->get($url);
+        
+        if($response->is_success) {
+            
+            # parse the data into a hash
+            for(grep {$_ !~ /hg_build/} split /\cJ/, $response->decoded_content) {
+                s/\"//g;
+                
+                my ($build, $pos, $gene, $acc, $dna, $url) = split /\t/;
+                
+                $data = join(',', $gene, $acc, $dna)
+            }
+            
+            $self->{lovd_cache}->{$locus} = $data;
+        }
+    }
+    else {
+        $data = $self->{lovd_cache}->{$locus};
+    }
+    
+    return $data ? { LOVD => $data } : {};
+}
+
+1;
+