diff variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/TranscriptEffect.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/TranscriptEffect.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,96 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2012 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
+
+ Please email comments or questions to the public Ensembl
+ developers list at <[e-mail]>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <[e-mail]>.
+
+=cut
+
+package Bio::EnsEMBL::Variation::Pipeline::TranscriptEffect;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::TranscriptVariation;
+use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(MAX_DISTANCE_FROM_TRANSCRIPT);
+
+use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);
+
+my $DEBUG   = 0;
+
+sub run {
+    my $self = shift;
+
+    my $transcript_id = $self->required_param('transcript_stable_id'); 
+
+    my $disambiguate_sn_alleles = 
+        $self->param('disambiguate_single_nucleotide_alleles'); 
+    
+    my $variations_to_include;
+    
+    if (my $vars = $self->param('variations_to_include')) {
+        # turn the list of variation names into a hash to speed up checking
+        $variations_to_include = { map { $_ => 1 } @$vars };
+    }
+
+    my $core_dba = $self->get_species_adaptor('core');
+    my $var_dba = $self->get_species_adaptor('variation');
+    
+    my $ta = $core_dba->get_TranscriptAdaptor;
+    my $sa = $core_dba->get_SliceAdaptor;
+    
+    my $tva = $var_dba->get_TranscriptVariationAdaptor;
+
+    my $transcript = $ta->fetch_by_stable_id($transcript_id) 
+        or die "failed to fetch transcript for stable id: $transcript_id";
+
+    # we need to include failed variations
+
+    $tva->db->include_failed_variations(1);
+
+    my $slice = $sa->fetch_by_transcript_stable_id(
+        $transcript->stable_id, 
+        MAX_DISTANCE_FROM_TRANSCRIPT
+    ) or die "failed to get slice around transcript: ".$transcript->stable_id;
+
+    for my $vf ( @{ $slice->get_all_VariationFeatures }, 
+                 @{ $slice->get_all_somatic_VariationFeatures } ) {
+
+        if (defined $variations_to_include) {
+            next unless $variations_to_include->{$vf->variation_name};
+        }
+
+        my $tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
+            -transcript         => $transcript,
+            -variation_feature  => $vf,
+            -adaptor            => $tva,
+            -disambiguate_single_nucleotide_alleles => $disambiguate_sn_alleles,
+        );
+
+        # if the variation has no effect on the transcript $tv will be undef
+
+        if ($tv && ( scalar(@{ $tv->consequence_type }) > 0) ) {
+            $tva->store($tv);
+        }
+    }
+
+    return;
+}
+
+sub write_output {
+    my $self = shift;
+}
+
+1;