diff dir_plugins/CSN.pm @ 0:e545d0a25ffe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/CSN.pm	Mon Jul 15 05:17:17 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
+
+  CSN
+
+=head1 SYNOPSIS
+
+  mv CSN.pm ~/.vep/Plugins
+  ./vep -i variations.vcf --cache --plugin CSN
+
+=head1 DESCRIPTION
+
+  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
+  reports Clinical Sequencing Nomenclature (CSN) for variants.
+
+  Each notation is given with reference to the transcript identifier;
+  specify "--plugin CSN,1" to remove this identifier from the CSN string.
+
+  You may also wish to specify "--no_escape" to prevent the "=" in "p.="
+  notations being converted to the URI-escaped equivalent "p.%3D"; doing
+  so may break parsers looking for "=" as a KEY=VALUE separator.
+
+  See http://biorxiv.org/content/early/2015/03/21/016808.1
+
+=cut
+
+package CSN;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+use Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor;
+use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub new {
+  my $class = shift;
+  
+  my $self = $class->SUPER::new(@_);
+  
+  # check config is OK
+  
+  # FASTA file defined, optimal
+  if(!defined($self->{config}->{fasta})) {
+    
+    # offline mode won't work without FASTA
+    die("ERROR: Cannot generate CSN without either a FASTA file (--fasta) or a database connection (--cache or --database)\n") if defined($self->{config}->{offline}) and !defined($self->{config}->{quiet});
+    
+    # cache mode will work, but DB will be accessed
+    warn("WARNING: Database will be accessed using this plugin; use a FASTA file (--fasta) for optimal performance") if defined($self->{config}->{cache}) and !defined($self->{config}->{quiet});
+  }
+  
+  no warnings 'once';
+  $Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = 1;
+  no warnings 'once';
+  $Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = 1;
+  
+  $self->{remove_transcript_ID} = $self->params->[0];
+  
+  return $self;
+}
+
+sub feature_types {
+  return ['Transcript'];
+}
+
+sub variant_feature_types {
+  return ['VariationFeature'];
+}
+
+sub get_header_info {
+  return { CSN => 'Clinical Sequencing Nomenclature'};
+}
+
+sub run {
+  my ($self, $tva) = @_;
+  
+  my ($hgvs_c, $hgvs_p) = ($tva->hgvs_transcript || '', $tva->hgvs_protein || '');
+  
+  return {} unless $hgvs_c;
+  
+  # trim off transcript/protein ID
+  $hgvs_c =~ s/.+\:// if $self->{remove_transcript_ID}; 
+  $hgvs_p =~ s/.+\://;
+  
+  # change Ter to X
+  $hgvs_p =~ s/Ter/X/g;
+  
+  # leave just p.=
+  $hgvs_p = 'p.=' if $hgvs_p =~ /p\.\=/;
+  
+  # escape
+  $hgvs_p =~ s/\=/\%3D/g unless $self->{config}->{no_escape};
+  
+  return { CSN => $hgvs_c.($hgvs_p ? '_'.$hgvs_p : '') };
+}
+
+1;