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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/GXA.pm	Mon Jul 15 05:20:39 2019 -0400
@@ -0,0 +1,165 @@
+=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
+
+  GXA
+
+=head1 SYNOPSIS
+
+  mv GXA.pm ~/.vep/Plugins
+  ./vep -i variations.vcf --cache --plugin GXA
+
+=head1 DESCRIPTION
+
+  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
+  reports data from the Gene Expression Atlas.
+
+  NB: no account is taken for comparing values across experiments; if values
+  exist for the same tissue in more than one experiment, the highest value
+  is reported.
+
+=cut
+
+package GXA;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub new {
+  my $class = shift;
+  
+  my $self = $class->SUPER::new(@_);
+
+  die("ERROR: This plugin is currently non-functional due to changes in the Gene Expression Atlas API");
+  
+  $self->{species} =  $self->{config}->{species};
+  $self->{species} =~ s/\_/\%20/;
+  
+  $self->{url} = 'https://www.ebi.ac.uk/gxa/widgets/heatmap/multiExperiment.tsv?propertyType=bioentity_identifier';
+  
+  return $self;
+}
+
+sub feature_types {
+  return ['Transcript'];
+}
+
+sub variant_feature_types {
+  return ['BaseVariationFeature'];
+}
+
+sub get_header_info {
+  my $self = shift;
+  
+  if(!exists($self->{_header_info})) {
+    
+    # get tissues using BRCA2
+    my $url = sprintf(
+      '%s&species=%s&geneQuery=%s',
+      $self->{url},
+      $self->{species},
+      'BRCA2'
+    );
+    
+    open IN, "curl -s \"$url\" |";
+    my @lines = <IN>;
+    
+    my %headers = ();
+    
+    while(my $line = shift @lines) {
+      next if $line =~ /^#/;
+      chomp $line;
+      $line =~ s/ /\_/g;
+      %headers = map {'GXA_'.$_ => "Tissue expression level in $_ from Gene Expression Atlas"} (split /\t/, $line);
+      last;
+    }
+    
+    close IN;
+    
+    $self->{_header_info} = \%headers;
+  };
+  
+  return $self->{_header_info};
+}
+
+sub run {
+  my ($self, $tva) = @_;
+  
+  my $tr = $tva->transcript;
+  my $gene_id = $tr->{_gene_stable_id} || $tr->{_gene}->stable_id;
+  return {} unless $gene_id;
+  
+  if(!exists($self->{_cache}) || !exists($self->{_cache}->{$gene_id})) {
+    
+    my $url = sprintf(
+      '%s&species=%s&geneQuery=%s',
+      $self->{url},
+      $self->{species},
+      $gene_id
+    );
+    
+    open IN, "curl -s \"$url\" |";
+    
+    my $first = 1;
+    my (@headers, %data);
+    
+    while(<IN>) {
+      next if /^#/;
+      chomp;
+            
+      if($first) {
+        s/ /\_/g;
+        @headers = split /\t/, $_;
+        $first = 0;
+      }
+      else {
+        my @tmp = split /\t/, $_;
+        
+        for(my $i=0; $i<=$#headers; $i++) {
+          my ($h, $d) = ('GXA_'.$headers[$i], $tmp[$i]);
+          next unless defined($d) && $d =~ /^[0-9\.]+$/;
+          
+          if(exists($data{$h})) {
+            $data{$h} = $d if $d > $data{$h};
+          }
+          else {
+            $data{$h} = $d;
+          }
+        }
+      }
+    }
+    
+    close IN;
+    
+    $self->{_cache}->{$gene_id} = \%data;
+  }
+  
+  return $self->{_cache}->{$gene_id};
+}
+
+1;